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- Committer: Bazaar Package Importer
- Author(s): Charles Plessy
- Date: 2008-03-18 14:44:57 UTC
- mfrom: (4 hardy)
- mto: This revision was merged to the branch mainline in revision 6.
- Revision ID: james.westby@ubuntu.com-20080318144457-1jjoztrvqwf0gruk
* debian/control:
- Removed MIA Matt Hope (dopey) from the Uploaders field.
Thank you for your work, Matt. I hope you are doing well.
- Downgraded some recommended package to the 'Suggests' priority,
according to the following discussion on Upstream's mail list.
http://bioperl.org/pipermail/bioperl-l/2008-March/027379.html
(Closes: #448890)
* debian/copyright converted to machine-readable format.
- Removed MIA Matt Hope (dopey) from the Uploaders field.
Thank you for your work, Matt. I hope you are doing well.
- Downgraded some recommended package to the 'Suggests' priority,
according to the following discussion on Upstream's mail list.
http://bioperl.org/pipermail/bioperl-l/2008-March/027379.html
(Closes: #448890)
* debian/copyright converted to machine-readable format.
- files added:
- Bio/Align/ProteinStatistics.pm
- Bio/DB/EUtilities
- Bio/DB/Expression
- Bio/DB/GFF/Adaptor/berkeleydb
- Bio/DB/GFF/Adaptor/memory
- Bio/DB/SeqFeature
- Bio/DB/SeqFeature/Store
- Bio/DB/SeqFeature/Store/DBI
- Bio/DB/SeqVersion
- Bio/FeatureIO
- Bio/Graph
- Bio/Graph/IO
- Bio/Graph/SimpleGraph
- Bio/Ontology/SimpleGOEngine
- Bio/SeqIO/tinyseq
- Bio/Tools/SiRNA
- Bio/Tools/SiRNA/Ruleset
- Bio/Tools/Spidey
- Bio/Tree/Draw
- debian/patches
- doc/Deobfuscator
- doc/Deobfuscator/bin
- doc/Deobfuscator/cgi-bin
- doc/Deobfuscator/lib
- doc/Deobfuscator/t
- examples/structure
- scripts/Bio-SeqFeature-Store
- scripts/biographics
- t/data/codeml_lysozyme
- t/data/seqfeaturedb
- t/data/taxdump
- t/lib
- t/lib/Test
- t/lib/Test/Builder
- t/lib/Test/Builder/Tester
- files removed:
- Bio/DB/GFF/Adaptor/memory_iterator.pm
- Bio/Tools/Blast
- doc/faq
- doc/howto
- doc/howto/examples
- doc/howto/examples/graphics
- doc/howto/figs
- doc/howto/figs/graphics
- doc/howto/html
- doc/howto/html/images
- doc/howto/pdf
- doc/howto/sgml
- doc/howto/txt
- files modified:
- AUTHORS
added
removed
Makefile.old
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# This Makefile is for the Bio extension to perl.
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#
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# It was generated automatically by MakeMaker version
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# 6.17 (Revision: 1.133) from the contents of
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# Makefile.PL. Don't edit this file, edit Makefile.PL instead.
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#
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# ANY CHANGES MADE HERE WILL BE LOST!
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#
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# MakeMaker ARGV: ()
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#
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# MakeMaker Parameters:
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# ABSTRACT => q[Bioinformatics Toolkit]
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# AUTHOR => q[Bioperl Team (bioperl-l@bioperl.org)]
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# DIR => []
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# DISTNAME => q[bioperl]
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# EXE_FILES => []
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# NAME => q[Bio]
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# PL_FILES => { doc/makedoc.PL=>[q[bioscripts.pod], q[biodatabases.pod], q[biodesign.pod], q[bioperl.pod]] }
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# PREREQ_PM => { IO::Scalar=>q[0], IO::String=>q[0], HTML::Entities=>q[0], File::Spec=>q[0], File::Temp=>q[0], DB_File=>q[0] }
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# VERSION_FROM => q[Bio/Root/Version.pm]
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# dist => { DIST_DEFAULT=>q[all tardist], COMPRESS=>q[gzip -9f], SUFFIX=>q[.gz] }
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# realclean => { FILES=>q[./Seq.pm.bak] }
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# --- MakeMaker post_initialize section:
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# --- MakeMaker const_config section:
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# These definitions are from config.sh (via /usr/lib/perl5/5.8.2/i386-linux-thread-multi/Config.pm)
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# They may have been overridden via Makefile.PL or on the command line
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AR = ar
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CC = gcc
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CCCDLFLAGS = -fPIC
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CCDLFLAGS = -rdynamic -Wl,-rpath,/usr/lib/perl5/5.8.2/i386-linux-thread-multi/CORE
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DLEXT = so
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DLSRC = dl_dlopen.xs
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LD = gcc
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LDDLFLAGS = -shared -L/usr/local/lib
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LDFLAGS = -L/usr/local/lib
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LIBC = /lib/libc-2.3.2.so
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LIB_EXT = .a
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OBJ_EXT = .o
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OSNAME = linux
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OSVERS = 2.4.21-6mdkenterprise
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RANLIB = :
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SITELIBEXP = /usr/lib/perl5/site_perl/5.8.2
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SITEARCHEXP = /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi
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SO = so
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EXE_EXT =
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FULL_AR = /usr/bin/ar
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VENDORARCHEXP = /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi
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VENDORLIBEXP = /usr/lib/perl5/vendor_perl/5.8.2
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# --- MakeMaker constants section:
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AR_STATIC_ARGS = cr
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DIRFILESEP = /
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NAME = Bio
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NAME_SYM = Bio
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VERSION = 1.4
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VERSION_MACRO = VERSION
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VERSION_SYM = 1_4
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DEFINE_VERSION = -D$(VERSION_MACRO)=\"$(VERSION)\"
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XS_VERSION = 1.4
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XS_VERSION_MACRO = XS_VERSION
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XS_DEFINE_VERSION = -D$(XS_VERSION_MACRO)=\"$(XS_VERSION)\"
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INST_ARCHLIB = blib/arch
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INST_SCRIPT = blib/script
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INST_BIN = blib/bin
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INST_LIB = blib/lib
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INST_MAN1DIR = blib/man1
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INST_MAN3DIR = blib/man3
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MAN1EXT = 1
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MAN3EXT = 3pm
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INSTALLDIRS = site
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DESTDIR =
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PREFIX =
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PERLPREFIX = /usr
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SITEPREFIX = /usr
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VENDORPREFIX = /usr
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INSTALLPRIVLIB = $(PERLPREFIX)/lib/perl5/5.8.2
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DESTINSTALLPRIVLIB = $(DESTDIR)$(INSTALLPRIVLIB)
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INSTALLSITELIB = $(SITEPREFIX)/lib/perl5/site_perl/5.8.2
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DESTINSTALLSITELIB = $(DESTDIR)$(INSTALLSITELIB)
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INSTALLVENDORLIB = $(VENDORPREFIX)/lib/perl5/vendor_perl/5.8.2
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DESTINSTALLVENDORLIB = $(DESTDIR)$(INSTALLVENDORLIB)
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INSTALLARCHLIB = $(PERLPREFIX)/lib/perl5/5.8.2/i386-linux-thread-multi
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DESTINSTALLARCHLIB = $(DESTDIR)$(INSTALLARCHLIB)
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INSTALLSITEARCH = $(SITEPREFIX)/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi
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DESTINSTALLSITEARCH = $(DESTDIR)$(INSTALLSITEARCH)
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INSTALLVENDORARCH = $(VENDORPREFIX)/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi
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DESTINSTALLVENDORARCH = $(DESTDIR)$(INSTALLVENDORARCH)
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INSTALLBIN = $(PERLPREFIX)/bin
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DESTINSTALLBIN = $(DESTDIR)$(INSTALLBIN)
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INSTALLSITEBIN = $(SITEPREFIX)/bin
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DESTINSTALLSITEBIN = $(DESTDIR)$(INSTALLSITEBIN)
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INSTALLVENDORBIN = $(VENDORPREFIX)/bin
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DESTINSTALLVENDORBIN = $(DESTDIR)$(INSTALLVENDORBIN)
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INSTALLSCRIPT = $(PERLPREFIX)/bin
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DESTINSTALLSCRIPT = $(DESTDIR)$(INSTALLSCRIPT)
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INSTALLMAN1DIR = $(PERLPREFIX)/share/man/man1
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DESTINSTALLMAN1DIR = $(DESTDIR)$(INSTALLMAN1DIR)
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INSTALLSITEMAN1DIR = $(SITEPREFIX)/share/man/man1
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DESTINSTALLSITEMAN1DIR = $(DESTDIR)$(INSTALLSITEMAN1DIR)
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INSTALLVENDORMAN1DIR = $(VENDORPREFIX)/share/man/man1
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DESTINSTALLVENDORMAN1DIR = $(DESTDIR)$(INSTALLVENDORMAN1DIR)
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INSTALLMAN3DIR = $(PERLPREFIX)/share/man/man3
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DESTINSTALLMAN3DIR = $(DESTDIR)$(INSTALLMAN3DIR)
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INSTALLSITEMAN3DIR = $(SITEPREFIX)/share/man/man3
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DESTINSTALLSITEMAN3DIR = $(DESTDIR)$(INSTALLSITEMAN3DIR)
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INSTALLVENDORMAN3DIR = $(VENDORPREFIX)/share/man/man3
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DESTINSTALLVENDORMAN3DIR = $(DESTDIR)$(INSTALLVENDORMAN3DIR)
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PERL_LIB = /usr/lib/perl5/5.8.2
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PERL_ARCHLIB = /usr/lib/perl5/5.8.2/i386-linux-thread-multi
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LIBPERL_A = libperl.a
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FIRST_MAKEFILE = Makefile
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MAKEFILE_OLD = $(FIRST_MAKEFILE).old
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MAKE_APERL_FILE = $(FIRST_MAKEFILE).aperl
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PERLMAINCC = $(CC)
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PERL_INC = /usr/lib/perl5/5.8.2/i386-linux-thread-multi/CORE
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PERL = /usr/bin/perl5.8.2
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FULLPERL = /usr/bin/perl5.8.2
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ABSPERL = $(PERL)
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PERLRUN = $(PERL)
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FULLPERLRUN = $(FULLPERL)
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ABSPERLRUN = $(ABSPERL)
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PERLRUNINST = $(PERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
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FULLPERLRUNINST = $(FULLPERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
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ABSPERLRUNINST = $(ABSPERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
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PERL_CORE = 0
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PERM_RW = 644
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PERM_RWX = 755
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MAKEMAKER = /usr/lib/perl5/5.8.2/ExtUtils/MakeMaker.pm
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MM_VERSION = 6.17
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MM_REVISION = 1.133
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# FULLEXT = Pathname for extension directory (eg Foo/Bar/Oracle).
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# BASEEXT = Basename part of FULLEXT. May be just equal FULLEXT. (eg Oracle)
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# PARENT_NAME = NAME without BASEEXT and no trailing :: (eg Foo::Bar)
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# DLBASE = Basename part of dynamic library. May be just equal BASEEXT.
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FULLEXT = Bio
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BASEEXT = Bio
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PARENT_NAME =
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DLBASE = $(BASEEXT)
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VERSION_FROM = Bio/Root/Version.pm
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OBJECT =
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LDFROM = $(OBJECT)
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LINKTYPE = dynamic
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# Handy lists of source code files:
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XS_FILES =
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C_FILES =
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O_FILES =
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H_FILES =
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MAN1PODS =
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MAN3PODS = Bio/Align/AlignI.pm \
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Bio/Align/DNAStatistics.pm \
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Bio/Align/PairwiseStatistics.pm \
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Bio/Align/StatisticsI.pm \
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Bio/Align/Utilities.pm \
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Bio/AlignIO.pm \
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Bio/AlignIO/bl2seq.pm \
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Bio/AlignIO/clustalw.pm \
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Bio/AlignIO/emboss.pm \
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Bio/AlignIO/fasta.pm \
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Bio/AlignIO/maf.pm \
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Bio/AlignIO/mase.pm \
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Bio/AlignIO/mega.pm \
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Bio/AlignIO/meme.pm \
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Bio/AlignIO/metafasta.pm \
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Bio/AlignIO/msf.pm \
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Bio/AlignIO/nexus.pm \
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Bio/AlignIO/pfam.pm \
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Bio/AlignIO/phylip.pm \
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Bio/AlignIO/prodom.pm \
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Bio/AlignIO/psi.pm \
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Bio/AlignIO/selex.pm \
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Bio/AlignIO/stockholm.pm \
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Bio/AnalysisI.pm \
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Bio/AnalysisParserI.pm \
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Bio/AnalysisResultI.pm \
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Bio/AnnotatableI.pm \
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Bio/Annotation/AnnotationFactory.pm \
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Bio/Annotation/Collection.pm \
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Bio/Annotation/Comment.pm \
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Bio/Annotation/DBLink.pm \
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Bio/Annotation/OntologyTerm.pm \
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Bio/Annotation/Reference.pm \
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Bio/Annotation/SimpleValue.pm \
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Bio/Annotation/StructuredValue.pm \
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Bio/Annotation/TypeManager.pm \
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Bio/AnnotationCollectionI.pm \
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Bio/AnnotationI.pm \
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Bio/Assembly/Contig.pm \
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Bio/Assembly/ContigAnalysis.pm \
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Bio/Assembly/IO.pm \
200
Bio/Assembly/IO/ace.pm \
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Bio/Assembly/IO/phrap.pm \
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Bio/Assembly/Scaffold.pm \
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Bio/Assembly/ScaffoldI.pm \
204
Bio/Biblio.pm \
205
Bio/Biblio/Article.pm \
206
Bio/Biblio/BiblioBase.pm \
207
Bio/Biblio/Book.pm \
208
Bio/Biblio/BookArticle.pm \
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Bio/Biblio/IO.pm \
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Bio/Biblio/IO/medline2ref.pm \
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Bio/Biblio/IO/medlinexml.pm \
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Bio/Biblio/IO/pubmed2ref.pm \
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Bio/Biblio/IO/pubmedxml.pm \
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Bio/Biblio/Journal.pm \
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Bio/Biblio/JournalArticle.pm \
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Bio/Biblio/MedlineArticle.pm \
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Bio/Biblio/MedlineBook.pm \
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Bio/Biblio/MedlineBookArticle.pm \
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Bio/Biblio/MedlineJournal.pm \
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Bio/Biblio/MedlineJournalArticle.pm \
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Bio/Biblio/Organisation.pm \
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Bio/Biblio/Patent.pm \
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Bio/Biblio/Person.pm \
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Bio/Biblio/Proceeding.pm \
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Bio/Biblio/Provider.pm \
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Bio/Biblio/PubmedArticle.pm \
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Bio/Biblio/PubmedBookArticle.pm \
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Bio/Biblio/PubmedJournalArticle.pm \
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Bio/Biblio/Ref.pm \
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Bio/Biblio/Service.pm \
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Bio/Biblio/TechReport.pm \
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Bio/Biblio/Thesis.pm \
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Bio/Biblio/WebResource.pm \
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Bio/Cluster/ClusterFactory.pm \
235
Bio/Cluster/FamilyI.pm \
236
Bio/Cluster/SequenceFamily.pm \
237
Bio/Cluster/UniGene.pm \
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Bio/Cluster/UniGeneI.pm \
239
Bio/ClusterI.pm \
240
Bio/ClusterIO.pm \
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Bio/ClusterIO/dbsnp.pm \
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Bio/ClusterIO/unigene.pm \
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Bio/CodonUsage/IO.pm \
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Bio/CodonUsage/Table.pm \
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Bio/Coordinate/Chain.pm \
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Bio/Coordinate/Collection.pm \
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Bio/Coordinate/ExtrapolatingPair.pm \
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Bio/Coordinate/GeneMapper.pm \
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Bio/Coordinate/Graph.pm \
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Bio/Coordinate/MapperI.pm \
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Bio/Coordinate/Pair.pm \
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Bio/Coordinate/Result.pm \
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Bio/Coordinate/Result/Gap.pm \
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Bio/Coordinate/Result/Match.pm \
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Bio/Coordinate/ResultI.pm \
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Bio/Coordinate/Utils.pm \
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Bio/DB/Ace.pm \
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Bio/DB/Biblio/biofetch.pm \
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Bio/DB/Biblio/soap.pm \
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Bio/DB/BiblioI.pm \
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Bio/DB/BioFetch.pm \
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Bio/DB/CUTG.pm \
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Bio/DB/DBFetch.pm \
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Bio/DB/EMBL.pm \
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Bio/DB/Failover.pm \
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Bio/DB/Fasta.pm \
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Bio/DB/FileCache.pm \
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Bio/DB/Flat.pm \
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Bio/DB/Flat/BDB.pm \
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Bio/DB/Flat/BDB/embl.pm \
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Bio/DB/Flat/BDB/fasta.pm \
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Bio/DB/Flat/BDB/genbank.pm \
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Bio/DB/Flat/BDB/swiss.pm \
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Bio/DB/Flat/BDB/swissprot.pm \
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Bio/DB/Flat/BinarySearch.pm \
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Bio/DB/GDB.pm \
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Bio/DB/GFF.pm \
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Bio/DB/GFF/Adaptor/ace.pm \
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Bio/DB/GFF/Adaptor/biofetch.pm \
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Bio/DB/GFF/Adaptor/biofetch_oracle.pm \
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Bio/DB/GFF/Adaptor/dbi.pm \
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Bio/DB/GFF/Adaptor/dbi/caching_handle.pm \
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Bio/DB/GFF/Adaptor/dbi/iterator.pm \
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Bio/DB/GFF/Adaptor/dbi/mysql.pm \
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Bio/DB/GFF/Adaptor/dbi/mysqlace.pm \
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Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm \
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Bio/DB/GFF/Adaptor/dbi/oracle.pm \
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Bio/DB/GFF/Adaptor/dbi/oracleace.pm \
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Bio/DB/GFF/Adaptor/dbi/pg.pm \
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Bio/DB/GFF/Adaptor/memory.pm \
291
Bio/DB/GFF/Adaptor/memory_iterator.pm \
292
Bio/DB/GFF/Aggregator.pm \
293
Bio/DB/GFF/Aggregator/alignment.pm \
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Bio/DB/GFF/Aggregator/clone.pm \
295
Bio/DB/GFF/Aggregator/coding.pm \
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Bio/DB/GFF/Aggregator/match.pm \
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Bio/DB/GFF/Aggregator/none.pm \
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Bio/DB/GFF/Aggregator/processed_transcript.pm \
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Bio/DB/GFF/Aggregator/transcript.pm \
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Bio/DB/GFF/Aggregator/ucsc_acembly.pm \
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Bio/DB/GFF/Aggregator/ucsc_ensgene.pm \
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Bio/DB/GFF/Aggregator/ucsc_genscan.pm \
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Bio/DB/GFF/Aggregator/ucsc_refgene.pm \
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Bio/DB/GFF/Aggregator/ucsc_sanger22.pm \
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Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm \
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Bio/DB/GFF/Aggregator/ucsc_softberry.pm \
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Bio/DB/GFF/Aggregator/ucsc_twinscan.pm \
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Bio/DB/GFF/Aggregator/ucsc_unigene.pm \
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Bio/DB/GFF/Featname.pm \
310
Bio/DB/GFF/Feature.pm \
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Bio/DB/GFF/Homol.pm \
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Bio/DB/GFF/RelSegment.pm \
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Bio/DB/GFF/Segment.pm \
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Bio/DB/GFF/Typename.pm \
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Bio/DB/GFF/Util/Binning.pm \
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Bio/DB/GFF/Util/Rearrange.pm \
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Bio/DB/GenBank.pm \
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Bio/DB/GenPept.pm \
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Bio/DB/InMemoryCache.pm \
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Bio/DB/MeSH.pm \
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Bio/DB/NCBIHelper.pm \
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Bio/DB/Query/GenBank.pm \
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Bio/DB/Query/WebQuery.pm \
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Bio/DB/QueryI.pm \
325
Bio/DB/RandomAccessI.pm \
326
Bio/DB/RefSeq.pm \
327
Bio/DB/Registry.pm \
328
Bio/DB/SeqI.pm \
329
Bio/DB/SwissProt.pm \
330
Bio/DB/Taxonomy.pm \
331
Bio/DB/Taxonomy/entrez.pm \
332
Bio/DB/Taxonomy/flatfile.pm \
333
Bio/DB/Universal.pm \
334
Bio/DB/UpdateableSeqI.pm \
335
Bio/DB/WebDBSeqI.pm \
336
Bio/DB/XEMBL.pm \
337
Bio/DB/XEMBLService.pm \
338
Bio/DBLinkContainerI.pm \
339
Bio/Das/FeatureTypeI.pm \
340
Bio/Das/SegmentI.pm \
341
Bio/DasI.pm \
342
Bio/DescribableI.pm \
343
Bio/Event/EventGeneratorI.pm \
344
Bio/Event/EventHandlerI.pm \
345
Bio/Expression/FeatureGroup.pm \
346
Bio/Expression/FeatureI.pm \
347
Bio/Factory/AnalysisI.pm \
348
Bio/Factory/ApplicationFactoryI.pm \
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Bio/Factory/DriverFactory.pm \
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Bio/Factory/FTLocationFactory.pm \
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Bio/Factory/HitFactoryI.pm \
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Bio/Factory/LocationFactoryI.pm \
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Bio/Factory/MapFactoryI.pm \
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Bio/Factory/ObjectBuilderI.pm \
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Bio/Factory/ObjectFactory.pm \
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Bio/Factory/ObjectFactoryI.pm \
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Bio/Factory/ResultFactoryI.pm \
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Bio/Factory/SeqAnalysisParserFactory.pm \
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Bio/Factory/SeqAnalysisParserFactoryI.pm \
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Bio/Factory/SequenceFactoryI.pm \
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Bio/Factory/SequenceProcessorI.pm \
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Bio/Factory/SequenceStreamI.pm \
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Bio/Factory/TreeFactoryI.pm \
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Bio/FeatureHolderI.pm \
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Bio/Graphics.pm \
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Bio/Graphics/ConfiguratorI.pm \
367
Bio/Graphics/Feature.pm \
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Bio/Graphics/FeatureFile.pm \
369
Bio/Graphics/FeatureFile/Iterator.pm \
370
Bio/Graphics/Glyph.pm \
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Bio/Graphics/Glyph/Factory.pm \
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Bio/Graphics/Glyph/alignment.pm \
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Bio/Graphics/Glyph/anchored_arrow.pm \
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Bio/Graphics/Glyph/arrow.pm \
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Bio/Graphics/Glyph/box.pm \
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Bio/Graphics/Glyph/cds.pm \
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Bio/Graphics/Glyph/crossbox.pm \
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Bio/Graphics/Glyph/diamond.pm \
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Bio/Graphics/Glyph/dna.pm \
380
Bio/Graphics/Glyph/dot.pm \
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Bio/Graphics/Glyph/ellipse.pm \
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Bio/Graphics/Glyph/ex.pm \
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Bio/Graphics/Glyph/extending_arrow.pm \
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Bio/Graphics/Glyph/generic.pm \
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Bio/Graphics/Glyph/graded_segments.pm \
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Bio/Graphics/Glyph/group.pm \
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Bio/Graphics/Glyph/heterogeneous_segments.pm \
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Bio/Graphics/Glyph/line.pm \
389
Bio/Graphics/Glyph/minmax.pm \
390
Bio/Graphics/Glyph/oval.pm \
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Bio/Graphics/Glyph/pinsertion.pm \
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Bio/Graphics/Glyph/primers.pm \
393
Bio/Graphics/Glyph/processed_transcript.pm \
394
Bio/Graphics/Glyph/redgreen_box.pm \
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Bio/Graphics/Glyph/redgreen_segment.pm \
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Bio/Graphics/Glyph/rndrect.pm \
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Bio/Graphics/Glyph/ruler_arrow.pm \
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Bio/Graphics/Glyph/segmented_keyglyph.pm \
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Bio/Graphics/Glyph/segments.pm \
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Bio/Graphics/Glyph/span.pm \
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Bio/Graphics/Glyph/splice_site.pm \
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Bio/Graphics/Glyph/toomany.pm \
403
Bio/Graphics/Glyph/track.pm \
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Bio/Graphics/Glyph/transcript.pm \
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Bio/Graphics/Glyph/transcript2.pm \
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Bio/Graphics/Glyph/translation.pm \
407
Bio/Graphics/Glyph/triangle.pm \
408
Bio/Graphics/Glyph/xyplot.pm \
409
Bio/Graphics/Panel.pm \
410
Bio/Graphics/Pictogram.pm \
411
Bio/Graphics/RendererI.pm \
412
Bio/IdCollectionI.pm \
413
Bio/IdentifiableI.pm \
414
Bio/Index/Abstract.pm \
415
Bio/Index/AbstractSeq.pm \
416
Bio/Index/Blast.pm \
417
Bio/Index/EMBL.pm \
418
Bio/Index/Fasta.pm \
419
Bio/Index/Fastq.pm \
420
Bio/Index/GenBank.pm \
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Bio/Index/SwissPfam.pm \
422
Bio/Index/Swissprot.pm \
423
Bio/LiveSeq/AARange.pm \
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Bio/LiveSeq/Chain.pm \
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Bio/LiveSeq/ChainI.pm \
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Bio/LiveSeq/DNA.pm \
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Bio/LiveSeq/Exon.pm \
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Bio/LiveSeq/Gene.pm \
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Bio/LiveSeq/IO/BioPerl.pm \
430
Bio/LiveSeq/IO/Loader.pm \
431
Bio/LiveSeq/IO/SRS.pm \
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Bio/LiveSeq/Intron.pm \
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Bio/LiveSeq/Mutation.pm \
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Bio/LiveSeq/Mutator.pm \
435
Bio/LiveSeq/Prim_Transcript.pm \
436
Bio/LiveSeq/Range.pm \
437
Bio/LiveSeq/Repeat_Region.pm \
438
Bio/LiveSeq/Repeat_Unit.pm \
439
Bio/LiveSeq/SeqI.pm \
440
Bio/LiveSeq/Transcript.pm \
441
Bio/LiveSeq/Translation.pm \
442
Bio/LocatableSeq.pm \
443
Bio/Location/Atomic.pm \
444
Bio/Location/AvWithinCoordPolicy.pm \
445
Bio/Location/CoordinatePolicyI.pm \
446
Bio/Location/Fuzzy.pm \
447
Bio/Location/FuzzyLocationI.pm \
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Bio/Location/NarrowestCoordPolicy.pm \
449
Bio/Location/Simple.pm \
450
Bio/Location/Split.pm \
451
Bio/Location/SplitLocationI.pm \
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Bio/Location/WidestCoordPolicy.pm \
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Bio/LocationI.pm \
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Bio/Map/CytoMap.pm \
455
Bio/Map/CytoMarker.pm \
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Bio/Map/CytoPosition.pm \
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Bio/Map/LinkageMap.pm \
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Bio/Map/LinkagePosition.pm \
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Bio/Map/MapI.pm \
460
Bio/Map/MappableI.pm \
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Bio/Map/Marker.pm \
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Bio/Map/MarkerI.pm \
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Bio/Map/Microsatellite.pm \
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Bio/Map/OrderedPosition.pm \
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Bio/Map/OrderedPositionWithDistance.pm \
466
Bio/Map/Position.pm \
467
Bio/Map/PositionI.pm \
468
Bio/Map/SimpleMap.pm \
469
Bio/MapIO.pm \
470
Bio/MapIO/mapmaker.pm \
471
Bio/Matrix/Generic.pm \
472
Bio/Matrix/IO.pm \
473
Bio/Matrix/IO/phylip.pm \
474
Bio/Matrix/IO/scoring.pm \
475
Bio/Matrix/MatrixI.pm \
476
Bio/Matrix/PSM/IO.pm \
477
Bio/Matrix/PSM/IO/mast.pm \
478
Bio/Matrix/PSM/IO/meme.pm \
479
Bio/Matrix/PSM/IO/transfac.pm \
480
Bio/Matrix/PSM/InstanceSite.pm \
481
Bio/Matrix/PSM/InstanceSiteI.pm \
482
Bio/Matrix/PSM/Psm.pm \
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Bio/Matrix/PSM/PsmHeader.pm \
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Bio/Matrix/PSM/PsmHeaderI.pm \
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Bio/Matrix/PSM/PsmI.pm \
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Bio/Matrix/PSM/SiteMatrix.pm \
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Bio/Matrix/PSM/SiteMatrixI.pm \
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Bio/Matrix/PhylipDist.pm \
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Bio/Matrix/Scoring.pm \
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Bio/Ontology/GOterm.pm \
491
Bio/Ontology/InterProTerm.pm \
492
Bio/Ontology/Ontology.pm \
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Bio/Ontology/OntologyEngineI.pm \
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Bio/Ontology/OntologyI.pm \
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Bio/Ontology/OntologyStore.pm \
496
Bio/Ontology/Path.pm \
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Bio/Ontology/PathI.pm \
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Bio/Ontology/Relationship.pm \
499
Bio/Ontology/RelationshipFactory.pm \
500
Bio/Ontology/RelationshipI.pm \
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Bio/Ontology/RelationshipType.pm \
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Bio/Ontology/SimpleGOEngine.pm \
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Bio/Ontology/SimpleOntologyEngine.pm \
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Bio/Ontology/Term.pm \
505
Bio/Ontology/TermFactory.pm \
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Bio/Ontology/TermI.pm \
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Bio/OntologyIO.pm \
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Bio/OntologyIO/Handlers/BaseSAXHandler.pm \
509
Bio/OntologyIO/Handlers/InterProHandler.pm \
510
Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm \
511
Bio/OntologyIO/InterProParser.pm \
512
Bio/OntologyIO/dagflat.pm \
513
Bio/OntologyIO/goflat.pm \
514
Bio/OntologyIO/simplehierarchy.pm \
515
Bio/OntologyIO/soflat.pm \
516
Bio/Perl.pm \
517
Bio/Phenotype/Correlate.pm \
518
Bio/Phenotype/MeSH/Term.pm \
519
Bio/Phenotype/MeSH/Twig.pm \
520
Bio/Phenotype/Measure.pm \
521
Bio/Phenotype/OMIM/MiniMIMentry.pm \
522
Bio/Phenotype/OMIM/OMIMentry.pm \
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Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm \
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Bio/Phenotype/OMIM/OMIMparser.pm \
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Bio/Phenotype/Phenotype.pm \
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Bio/Phenotype/PhenotypeI.pm \
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Bio/PopGen/Genotype.pm \
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Bio/PopGen/GenotypeI.pm \
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Bio/PopGen/IO.pm \
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Bio/PopGen/IO/csv.pm \
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Bio/PopGen/IO/prettybase.pm \
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Bio/PopGen/Individual.pm \
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Bio/PopGen/IndividualI.pm \
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Bio/PopGen/Marker.pm \
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Bio/PopGen/MarkerI.pm \
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Bio/PopGen/PopStats.pm \
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Bio/PopGen/Population.pm \
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Bio/PopGen/PopulationI.pm \
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Bio/PopGen/Simulation/Coalescent.pm \
540
Bio/PopGen/Simulation/GeneticDrift.pm \
541
Bio/PopGen/Statistics.pm \
542
Bio/PrimarySeq.pm \
543
Bio/PrimarySeqI.pm \
544
Bio/Range.pm \
545
Bio/RangeI.pm \
546
Bio/Restriction/Analysis.pm \
547
Bio/Restriction/Enzyme.pm \
548
Bio/Restriction/Enzyme/MultiCut.pm \
549
Bio/Restriction/Enzyme/MultiSite.pm \
550
Bio/Restriction/EnzymeCollection.pm \
551
Bio/Restriction/EnzymeI.pm \
552
Bio/Restriction/IO.pm \
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Bio/Restriction/IO/bairoch.pm \
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Bio/Restriction/IO/base.pm \
555
Bio/Restriction/IO/itype2.pm \
556
Bio/Restriction/IO/withrefm.pm \
557
Bio/Root/Err.pm \
558
Bio/Root/Exception.pm \
559
Bio/Root/Global.pm \
560
Bio/Root/HTTPget.pm \
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Bio/Root/IO.pm \
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Bio/Root/IOManager.pm \
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Bio/Root/Object.pm \
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Bio/Root/Root.pm \
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Bio/Root/RootI.pm \
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Bio/Root/Storable.pm \
567
Bio/Root/Utilities.pm \
568
Bio/Root/Vector.pm \
569
Bio/Root/Version.pm \
570
Bio/Root/Xref.pm \
571
Bio/Search/BlastUtils.pm \
572
Bio/Search/DatabaseI.pm \
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Bio/Search/GenericDatabase.pm \
574
Bio/Search/HSP/BlastHSP.pm \
575
Bio/Search/HSP/FastaHSP.pm \
576
Bio/Search/HSP/GenericHSP.pm \
577
Bio/Search/HSP/HMMERHSP.pm \
578
Bio/Search/HSP/HSPFactory.pm \
579
Bio/Search/HSP/HSPI.pm \
580
Bio/Search/HSP/PSLHSP.pm \
581
Bio/Search/HSP/PsiBlastHSP.pm \
582
Bio/Search/HSP/WABAHSP.pm \
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Bio/Search/Hit/BlastHit.pm \
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Bio/Search/Hit/Fasta.pm \
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Bio/Search/Hit/GenericHit.pm \
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Bio/Search/Hit/HMMERHit.pm \
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Bio/Search/Hit/HitFactory.pm \
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Bio/Search/Hit/HitI.pm \
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Bio/Search/Hit/PsiBlastHit.pm \
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Bio/Search/Iteration/GenericIteration.pm \
591
Bio/Search/Iteration/IterationI.pm \
592
Bio/Search/Processor.pm \
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Bio/Search/Result/BlastResult.pm \
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Bio/Search/Result/GenericResult.pm \
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Bio/Search/Result/HMMERResult.pm \
596
Bio/Search/Result/ResultFactory.pm \
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Bio/Search/Result/ResultI.pm \
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Bio/Search/Result/WABAResult.pm \
599
Bio/Search/SearchUtils.pm \
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Bio/SearchDist.pm \
601
Bio/SearchIO.pm \
602
Bio/SearchIO/EventHandlerI.pm \
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Bio/SearchIO/FastHitEventBuilder.pm \
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Bio/SearchIO/IteratedSearchResultEventBuilder.pm \
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Bio/SearchIO/SearchResultEventBuilder.pm \
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Bio/SearchIO/SearchWriterI.pm \
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Bio/SearchIO/Writer/BSMLResultWriter.pm \
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Bio/SearchIO/Writer/GbrowseGFF.pm \
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Bio/SearchIO/Writer/HSPTableWriter.pm \
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Bio/SearchIO/Writer/HTMLResultWriter.pm \
611
Bio/SearchIO/Writer/HitTableWriter.pm \
612
Bio/SearchIO/Writer/ResultTableWriter.pm \
613
Bio/SearchIO/Writer/TextResultWriter.pm \
614
Bio/SearchIO/axt.pm \
615
Bio/SearchIO/blast.pm \
616
Bio/SearchIO/blasttable.pm \
617
Bio/SearchIO/blastxml.pm \
618
Bio/SearchIO/exonerate.pm \
619
Bio/SearchIO/fasta.pm \
620
Bio/SearchIO/hmmer.pm \
621
Bio/SearchIO/megablast.pm \
622
Bio/SearchIO/psl.pm \
623
Bio/SearchIO/sim4.pm \
624
Bio/SearchIO/waba.pm \
625
Bio/SearchIO/wise.pm \
626
Bio/Seq.pm \
627
Bio/Seq/BaseSeqProcessor.pm \
628
Bio/Seq/EncodedSeq.pm \
629
Bio/Seq/LargePrimarySeq.pm \
630
Bio/Seq/LargeSeq.pm \
631
Bio/Seq/Meta.pm \
632
Bio/Seq/Meta/Array.pm \
633
Bio/Seq/MetaI.pm \
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Bio/Seq/PrimaryQual.pm \
635
Bio/Seq/PrimedSeq.pm \
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Bio/Seq/QualI.pm \
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Bio/Seq/RichSeq.pm \
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Bio/Seq/RichSeqI.pm \
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Bio/Seq/SeqBuilder.pm \
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Bio/Seq/SeqFactory.pm \
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Bio/Seq/SeqFastaSpeedFactory.pm \
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Bio/Seq/SeqWithQuality.pm \
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Bio/Seq/SequenceTrace.pm \
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Bio/Seq/TraceI.pm \
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Bio/SeqAnalysisParserI.pm \
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Bio/SeqFeature/AnnotationAdaptor.pm \
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Bio/SeqFeature/Collection.pm \
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Bio/SeqFeature/CollectionI.pm \
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Bio/SeqFeature/Computation.pm \
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Bio/SeqFeature/FeaturePair.pm \
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Bio/SeqFeature/Gene/Exon.pm \
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Bio/SeqFeature/Gene/ExonI.pm \
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Bio/SeqFeature/Gene/GeneStructure.pm \
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Bio/SeqFeature/Gene/GeneStructureI.pm \
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Bio/SeqFeature/Gene/Intron.pm \
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Bio/SeqFeature/Gene/NC_Feature.pm \
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Bio/SeqFeature/Gene/Poly_A_site.pm \
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Bio/SeqFeature/Gene/Promoter.pm \
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Bio/SeqFeature/Gene/Transcript.pm \
660
Bio/SeqFeature/Gene/TranscriptI.pm \
661
Bio/SeqFeature/Gene/UTR.pm \
662
Bio/SeqFeature/Generic.pm \
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Bio/SeqFeature/PositionProxy.pm \
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Bio/SeqFeature/Primer.pm \
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Bio/SeqFeature/SiRNA/Oligo.pm \
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Bio/SeqFeature/SiRNA/Pair.pm \
667
Bio/SeqFeature/Similarity.pm \
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Bio/SeqFeature/SimilarityPair.pm \
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Bio/SeqFeature/Tools/TypeMapper.pm \
670
Bio/SeqFeature/Tools/Unflattener.pm \
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Bio/SeqFeatureI.pm \
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Bio/SeqI.pm \
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Bio/SeqIO.pm \
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Bio/SeqIO/FTHelper.pm \
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Bio/SeqIO/MultiFile.pm \
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Bio/SeqIO/abi.pm \
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Bio/SeqIO/ace.pm \
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Bio/SeqIO/alf.pm \
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Bio/SeqIO/asciitree.pm \
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Bio/SeqIO/bsml.pm \
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Bio/SeqIO/chadoxml.pm \
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Bio/SeqIO/ctf.pm \
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Bio/SeqIO/embl.pm \
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Bio/SeqIO/exp.pm \
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Bio/SeqIO/fasta.pm \
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Bio/SeqIO/fastq.pm \
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Bio/SeqIO/game.pm \
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Bio/SeqIO/game/featHandler.pm \
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Bio/SeqIO/game/gameHandler.pm \
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Bio/SeqIO/game/gameSubs.pm \
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Bio/SeqIO/game/gameWriter.pm \
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Bio/SeqIO/game/seqHandler.pm \
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Bio/SeqIO/gcg.pm \
694
Bio/SeqIO/genbank.pm \
695
Bio/SeqIO/kegg.pm \
696
Bio/SeqIO/largefasta.pm \
697
Bio/SeqIO/locuslink.pm \
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Bio/SeqIO/metafasta.pm \
699
Bio/SeqIO/phd.pm \
700
Bio/SeqIO/pir.pm \
701
Bio/SeqIO/pln.pm \
702
Bio/SeqIO/qual.pm \
703
Bio/SeqIO/raw.pm \
704
Bio/SeqIO/scf.pm \
705
Bio/SeqIO/swiss.pm \
706
Bio/SeqIO/tab.pm \
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Bio/SeqIO/tigr.pm \
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Bio/SeqIO/ztr.pm \
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Bio/SeqUtils.pm \
710
Bio/SimpleAlign.pm \
711
Bio/SimpleAnalysisI.pm \
712
Bio/Species.pm \
713
Bio/Structure/Atom.pm \
714
Bio/Structure/Chain.pm \
715
Bio/Structure/Entry.pm \
716
Bio/Structure/IO.pm \
717
Bio/Structure/IO/pdb.pm \
718
Bio/Structure/Model.pm \
719
Bio/Structure/Residue.pm \
720
Bio/Structure/SecStr/DSSP/Res.pm \
721
Bio/Structure/SecStr/STRIDE/Res.pm \
722
Bio/Structure/StructureI.pm \
723
Bio/Symbol/Alphabet.pm \
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Bio/Symbol/AlphabetI.pm \
725
Bio/Symbol/DNAAlphabet.pm \
726
Bio/Symbol/ProteinAlphabet.pm \
727
Bio/Symbol/Symbol.pm \
728
Bio/Symbol/SymbolI.pm \
729
Bio/Taxonomy.pm \
730
Bio/Taxonomy/FactoryI.pm \
731
Bio/Taxonomy/Node.pm \
732
Bio/Taxonomy/Taxon.pm \
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Bio/Taxonomy/Tree.pm \
734
Bio/Tools/AlignFactory.pm \
735
Bio/Tools/Alignment/Consed.pm \
736
Bio/Tools/Alignment/Trim.pm \
737
Bio/Tools/Analysis/DNA/ESEfinder.pm \
738
Bio/Tools/Analysis/Protein/Domcut.pm \
739
Bio/Tools/Analysis/Protein/ELM.pm \
740
Bio/Tools/Analysis/Protein/GOR4.pm \
741
Bio/Tools/Analysis/Protein/HNN.pm \
742
Bio/Tools/Analysis/Protein/Mitoprot.pm \
743
Bio/Tools/Analysis/Protein/NetPhos.pm \
744
Bio/Tools/Analysis/Protein/Scansite.pm \
745
Bio/Tools/Analysis/Protein/Sopma.pm \
746
Bio/Tools/Analysis/SimpleAnalysisBase.pm \
747
Bio/Tools/AnalysisResult.pm \
748
Bio/Tools/BPbl2seq.pm \
749
Bio/Tools/BPlite.pm \
750
Bio/Tools/BPlite/HSP.pm \
751
Bio/Tools/BPlite/Iteration.pm \
752
Bio/Tools/BPlite/Sbjct.pm \
753
Bio/Tools/BPpsilite.pm \
754
Bio/Tools/Blast.pm \
755
Bio/Tools/Blast/HSP.pm \
756
Bio/Tools/Blast/HTML.pm \
757
Bio/Tools/Blast/Sbjct.pm \
758
Bio/Tools/Blat.pm \
759
Bio/Tools/CodonTable.pm \
760
Bio/Tools/Coil.pm \
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Bio/Tools/ECnumber.pm \
762
Bio/Tools/EMBOSS/Palindrome.pm \
763
Bio/Tools/EPCR.pm \
764
Bio/Tools/ESTScan.pm \
765
Bio/Tools/Eponine.pm \
766
Bio/Tools/Est2Genome.pm \
767
Bio/Tools/FootPrinter.pm \
768
Bio/Tools/GFF.pm \
769
Bio/Tools/Gel.pm \
770
Bio/Tools/Geneid.pm \
771
Bio/Tools/Genemark.pm \
772
Bio/Tools/Genewise.pm \
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Bio/Tools/Genomewise.pm \
774
Bio/Tools/Genscan.pm \
775
Bio/Tools/Glimmer.pm \
776
Bio/Tools/Grail.pm \
777
Bio/Tools/GuessSeqFormat.pm \
778
Bio/Tools/HMMER/Domain.pm \
779
Bio/Tools/HMMER/Results.pm \
780
Bio/Tools/HMMER/Set.pm \
781
Bio/Tools/Hmmpfam.pm \
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Bio/Tools/IUPAC.pm \
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Bio/Tools/Lucy.pm \
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Bio/Tools/MZEF.pm \
785
Bio/Tools/OddCodes.pm \
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Bio/Tools/Phylo/Molphy.pm \
787
Bio/Tools/Phylo/Molphy/Result.pm \
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Bio/Tools/Phylo/PAML.pm \
789
Bio/Tools/Phylo/PAML/ModelResult.pm \
790
Bio/Tools/Phylo/PAML/Result.pm \
791
Bio/Tools/Phylo/Phylip/ProtDist.pm \
792
Bio/Tools/Prediction/Exon.pm \
793
Bio/Tools/Prediction/Gene.pm \
794
Bio/Tools/Primer/Assessor/Base.pm \
795
Bio/Tools/Primer/AssessorI.pm \
796
Bio/Tools/Primer/Feature.pm \
797
Bio/Tools/Primer/Pair.pm \
798
Bio/Tools/Primer3.pm \
799
Bio/Tools/Prints.pm \
800
Bio/Tools/Profile.pm \
801
Bio/Tools/Promoterwise.pm \
802
Bio/Tools/PrositeScan.pm \
803
Bio/Tools/Pseudowise.pm \
804
Bio/Tools/QRNA.pm \
805
Bio/Tools/RandomDistFunctions.pm \
806
Bio/Tools/RepeatMasker.pm \
807
Bio/Tools/RestrictionEnzyme.pm \
808
Bio/Tools/Run/RemoteBlast.pm \
809
Bio/Tools/Run/StandAloneBlast.pm \
810
Bio/Tools/Run/WrapperBase.pm \
811
Bio/Tools/Seg.pm \
812
Bio/Tools/SeqAnal.pm \
813
Bio/Tools/SeqPattern.pm \
814
Bio/Tools/SeqStats.pm \
815
Bio/Tools/SeqWords.pm \
816
Bio/Tools/SiRNA.pm \
817
Bio/Tools/Sigcleave.pm \
818
Bio/Tools/Signalp.pm \
819
Bio/Tools/Sim4/Exon.pm \
820
Bio/Tools/Sim4/Results.pm \
821
Bio/Tools/Tmhmm.pm \
822
Bio/Tools/WWW.pm \
823
Bio/Tools/dpAlign.pm \
824
Bio/Tools/pICalculator.pm \
825
Bio/Tools/pSW.pm \
826
Bio/Tree/AlleleNode.pm \
827
Bio/Tree/Node.pm \
828
Bio/Tree/NodeI.pm \
829
Bio/Tree/NodeNHX.pm \
830
Bio/Tree/RandomFactory.pm \
831
Bio/Tree/Statistics.pm \
832
Bio/Tree/Tree.pm \
833
Bio/Tree/TreeFunctionsI.pm \
834
Bio/Tree/TreeI.pm \
835
Bio/TreeIO.pm \
836
Bio/TreeIO/TreeEventBuilder.pm \
837
Bio/TreeIO/lintree.pm \
838
Bio/TreeIO/newick.pm \
839
Bio/TreeIO/nexus.pm \
840
Bio/TreeIO/nhx.pm \
841
Bio/TreeIO/svggraph.pm \
842
Bio/TreeIO/tabtree.pm \
843
Bio/UpdateableSeqI.pm \
844
Bio/Variation/AAChange.pm \
845
Bio/Variation/AAReverseMutate.pm \
846
Bio/Variation/Allele.pm \
847
Bio/Variation/DNAMutation.pm \
848
Bio/Variation/IO.pm \
849
Bio/Variation/IO/flat.pm \
850
Bio/Variation/IO/xml.pm \
851
Bio/Variation/RNAChange.pm \
852
Bio/Variation/SNP.pm \
853
Bio/Variation/SeqDiff.pm \
854
Bio/Variation/VariantI.pm \
855
Bio/WebAgent.pm \
856
biodatabases.pod \
857
biodesign.pod \
858
bioperl.pod \
859
bioscripts.pod \
860
bptutorial.pl
861
862
# Where is the Config information that we are using/depend on
863
CONFIGDEP = $(PERL_ARCHLIB)$(DIRFILESEP)Config.pm $(PERL_INC)$(DIRFILESEP)config.h
864
865
# Where to build things
866
INST_LIBDIR = $(INST_LIB)
867
INST_ARCHLIBDIR = $(INST_ARCHLIB)
868
869
INST_AUTODIR = $(INST_LIB)/auto/$(FULLEXT)
870
INST_ARCHAUTODIR = $(INST_ARCHLIB)/auto/$(FULLEXT)
871
872
INST_STATIC =
873
INST_DYNAMIC =
874
INST_BOOT =
875
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# Extra linker info
877
EXPORT_LIST =
878
PERL_ARCHIVE =
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PERL_ARCHIVE_AFTER =
880
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TO_INST_PM = Bio/Align/AlignI.pm \
883
Bio/Align/DNAStatistics.pm \
884
Bio/Align/PairwiseStatistics.pm \
885
Bio/Align/StatisticsI.pm \
886
Bio/Align/Utilities.pm \
887
Bio/AlignIO.pm \
888
Bio/AlignIO/bl2seq.pm \
889
Bio/AlignIO/clustalw.pm \
890
Bio/AlignIO/emboss.pm \
891
Bio/AlignIO/fasta.pm \
892
Bio/AlignIO/maf.pm \
893
Bio/AlignIO/mase.pm \
894
Bio/AlignIO/mega.pm \
895
Bio/AlignIO/meme.pm \
896
Bio/AlignIO/metafasta.pm \
897
Bio/AlignIO/msf.pm \
898
Bio/AlignIO/nexus.pm \
899
Bio/AlignIO/pfam.pm \
900
Bio/AlignIO/phylip.pm \
901
Bio/AlignIO/prodom.pm \
902
Bio/AlignIO/psi.pm \
903
Bio/AlignIO/selex.pm \
904
Bio/AlignIO/stockholm.pm \
905
Bio/AnalysisI.pm \
906
Bio/AnalysisParserI.pm \
907
Bio/AnalysisResultI.pm \
908
Bio/AnnotatableI.pm \
909
Bio/Annotation/AnnotationFactory.pm \
910
Bio/Annotation/Collection.pm \
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Bio/Annotation/Comment.pm \
912
Bio/Annotation/DBLink.pm \
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Bio/Annotation/OntologyTerm.pm \
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Bio/Annotation/Reference.pm \
915
Bio/Annotation/SimpleValue.pm \
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Bio/Annotation/StructuredValue.pm \
917
Bio/Annotation/TypeManager.pm \
918
Bio/AnnotationCollectionI.pm \
919
Bio/AnnotationI.pm \
920
Bio/Assembly/Contig.pm \
921
Bio/Assembly/ContigAnalysis.pm \
922
Bio/Assembly/IO.pm \
923
Bio/Assembly/IO/ace.pm \
924
Bio/Assembly/IO/phrap.pm \
925
Bio/Assembly/Scaffold.pm \
926
Bio/Assembly/ScaffoldI.pm \
927
Bio/Biblio.pm \
928
Bio/Biblio/Article.pm \
929
Bio/Biblio/BiblioBase.pm \
930
Bio/Biblio/Book.pm \
931
Bio/Biblio/BookArticle.pm \
932
Bio/Biblio/IO.pm \
933
Bio/Biblio/IO/medline2ref.pm \
934
Bio/Biblio/IO/medlinexml.pm \
935
Bio/Biblio/IO/pubmed2ref.pm \
936
Bio/Biblio/IO/pubmedxml.pm \
937
Bio/Biblio/Journal.pm \
938
Bio/Biblio/JournalArticle.pm \
939
Bio/Biblio/MedlineArticle.pm \
940
Bio/Biblio/MedlineBook.pm \
941
Bio/Biblio/MedlineBookArticle.pm \
942
Bio/Biblio/MedlineJournal.pm \
943
Bio/Biblio/MedlineJournalArticle.pm \
944
Bio/Biblio/Organisation.pm \
945
Bio/Biblio/Patent.pm \
946
Bio/Biblio/Person.pm \
947
Bio/Biblio/Proceeding.pm \
948
Bio/Biblio/Provider.pm \
949
Bio/Biblio/PubmedArticle.pm \
950
Bio/Biblio/PubmedBookArticle.pm \
951
Bio/Biblio/PubmedJournalArticle.pm \
952
Bio/Biblio/Ref.pm \
953
Bio/Biblio/Service.pm \
954
Bio/Biblio/TechReport.pm \
955
Bio/Biblio/Thesis.pm \
956
Bio/Biblio/WebResource.pm \
957
Bio/Cluster/ClusterFactory.pm \
958
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Bio/DB/GFF/Adaptor/ace.pm \
2733
$(INST_LIB)/Bio/DB/GFF/Adaptor/ace.pm \
2734
Bio/LiveSeq/IO/README \
2735
$(INST_LIB)/Bio/LiveSeq/IO/README \
2736
Bio/Structure/SecStr/STRIDE/Res.pm \
2737
$(INST_LIB)/Bio/Structure/SecStr/STRIDE/Res.pm \
2738
Bio/Biblio/MedlineBookArticle.pm \
2739
$(INST_LIB)/Bio/Biblio/MedlineBookArticle.pm \
2740
Bio/Graphics/Glyph/ruler_arrow.pm \
2741
$(INST_LIB)/Bio/Graphics/Glyph/ruler_arrow.pm \
2742
Bio/Tools/Genemark.pm \
2743
$(INST_LIB)/Bio/Tools/Genemark.pm \
2744
Bio/Biblio/Patent.pm \
2745
$(INST_LIB)/Bio/Biblio/Patent.pm \
2746
Bio/Matrix/IO.pm \
2747
$(INST_LIB)/Bio/Matrix/IO.pm \
2748
Bio/DB/GFF/Aggregator.pm \
2749
$(INST_LIB)/Bio/DB/GFF/Aggregator.pm \
2750
Bio/Seq/RichSeq.pm \
2751
$(INST_LIB)/Bio/Seq/RichSeq.pm \
2752
Bio/SeqFeature/SiRNA/Pair.pm \
2753
$(INST_LIB)/Bio/SeqFeature/SiRNA/Pair.pm \
2754
Bio/DB/GFF.pm \
2755
$(INST_LIB)/Bio/DB/GFF.pm \
2756
Bio/Tools/BPpsilite.pm \
2757
$(INST_LIB)/Bio/Tools/BPpsilite.pm \
2758
Bio/Graphics/Glyph/track.pm \
2759
$(INST_LIB)/Bio/Graphics/Glyph/track.pm \
2760
Bio/PopGen/Simulation/GeneticDrift.pm \
2761
$(INST_LIB)/Bio/PopGen/Simulation/GeneticDrift.pm \
2762
Bio/Factory/ResultFactoryI.pm \
2763
$(INST_LIB)/Bio/Factory/ResultFactoryI.pm \
2764
Bio/SeqFeature/CollectionI.pm \
2765
$(INST_LIB)/Bio/SeqFeature/CollectionI.pm \
2766
Bio/Biblio/MedlineArticle.pm \
2767
$(INST_LIB)/Bio/Biblio/MedlineArticle.pm \
2768
Bio/Taxonomy/Taxon.pm \
2769
$(INST_LIB)/Bio/Taxonomy/Taxon.pm \
2770
Bio/AlignIO/metafasta.pm \
2771
$(INST_LIB)/Bio/AlignIO/metafasta.pm \
2772
Bio/Phenotype/PhenotypeI.pm \
2773
$(INST_LIB)/Bio/Phenotype/PhenotypeI.pm \
2774
Bio/Seq/LargeSeq.pm \
2775
$(INST_LIB)/Bio/Seq/LargeSeq.pm \
2776
Bio/DB/GDB.pm \
2777
$(INST_LIB)/Bio/DB/GDB.pm \
2778
Bio/Tools/Profile.pm \
2779
$(INST_LIB)/Bio/Tools/Profile.pm \
2780
Bio/Seq/EncodedSeq.pm \
2781
$(INST_LIB)/Bio/Seq/EncodedSeq.pm \
2782
Bio/Tools/Analysis/Protein/Domcut.pm \
2783
$(INST_LIB)/Bio/Tools/Analysis/Protein/Domcut.pm \
2784
Bio/Variation/README \
2785
$(INST_LIB)/Bio/Variation/README \
2786
Bio/DB/Registry.pm \
2787
$(INST_LIB)/Bio/DB/Registry.pm \
2788
bioscripts.pod \
2789
$(INST_LIB)/bioscripts.pod \
2790
Bio/Variation/VariantI.pm \
2791
$(INST_LIB)/Bio/Variation/VariantI.pm \
2792
Bio/Tools/Glimmer.pm \
2793
$(INST_LIB)/Bio/Tools/Glimmer.pm \
2794
Bio/Factory/SequenceFactoryI.pm \
2795
$(INST_LIB)/Bio/Factory/SequenceFactoryI.pm \
2796
Bio/Graphics/Glyph/line.pm \
2797
$(INST_LIB)/Bio/Graphics/Glyph/line.pm \
2798
Bio/Root/Utilities.pm \
2799
$(INST_LIB)/Bio/Root/Utilities.pm \
2800
Bio/Search/Hit/GenericHit.pm \
2801
$(INST_LIB)/Bio/Search/Hit/GenericHit.pm \
2802
Bio/Tools/RestrictionEnzyme.pm \
2803
$(INST_LIB)/Bio/Tools/RestrictionEnzyme.pm \
2804
Bio/Map/LinkageMap.pm \
2805
$(INST_LIB)/Bio/Map/LinkageMap.pm \
2806
Bio/AlignIO/stockholm.pm \
2807
$(INST_LIB)/Bio/AlignIO/stockholm.pm \
2808
Bio/OntologyIO/Handlers/InterProHandler.pm \
2809
$(INST_LIB)/Bio/OntologyIO/Handlers/InterProHandler.pm \
2810
Bio/DB/GFF/Adaptor/dbi/mysqlace.pm \
2811
$(INST_LIB)/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm \
2812
Bio/PopGen/Individual.pm \
2813
$(INST_LIB)/Bio/PopGen/Individual.pm \
2814
Bio/Seq/MetaI.pm \
2815
$(INST_LIB)/Bio/Seq/MetaI.pm \
2816
Bio/SeqFeature/Computation.pm \
2817
$(INST_LIB)/Bio/SeqFeature/Computation.pm \
2818
Bio/Tools/Analysis/Protein/Mitoprot.pm \
2819
$(INST_LIB)/Bio/Tools/Analysis/Protein/Mitoprot.pm \
2820
Bio/DasI.pm \
2821
$(INST_LIB)/Bio/DasI.pm \
2822
Bio/Graphics/Glyph/splice_site.pm \
2823
$(INST_LIB)/Bio/Graphics/Glyph/splice_site.pm \
2824
Bio/TreeIO/nhx.pm \
2825
$(INST_LIB)/Bio/TreeIO/nhx.pm \
2826
Bio/SeqUtils.pm \
2827
$(INST_LIB)/Bio/SeqUtils.pm \
2828
Bio/Assembly/Contig.pm \
2829
$(INST_LIB)/Bio/Assembly/Contig.pm \
2830
Bio/Assembly/Scaffold.pm \
2831
$(INST_LIB)/Bio/Assembly/Scaffold.pm \
2832
Bio/OntologyIO/simplehierarchy.pm \
2833
$(INST_LIB)/Bio/OntologyIO/simplehierarchy.pm \
2834
Bio/Structure/Residue.pm \
2835
$(INST_LIB)/Bio/Structure/Residue.pm \
2836
Bio/Tools/Sim4/Results.pm \
2837
$(INST_LIB)/Bio/Tools/Sim4/Results.pm \
2838
Bio/DB/GFF/Adaptor/dbi/iterator.pm \
2839
$(INST_LIB)/Bio/DB/GFF/Adaptor/dbi/iterator.pm \
2840
Bio/OntologyIO/Handlers/BaseSAXHandler.pm \
2841
$(INST_LIB)/Bio/OntologyIO/Handlers/BaseSAXHandler.pm \
2842
Bio/Variation/AAChange.pm \
2843
$(INST_LIB)/Bio/Variation/AAChange.pm \
2844
Bio/Index/Fastq.pm \
2845
$(INST_LIB)/Bio/Index/Fastq.pm \
2846
Bio/SearchIO/Writer/TextResultWriter.pm \
2847
$(INST_LIB)/Bio/SearchIO/Writer/TextResultWriter.pm \
2848
Bio/Range.pm \
2849
$(INST_LIB)/Bio/Range.pm \
2850
Bio/OntologyIO/dagflat.pm \
2851
$(INST_LIB)/Bio/OntologyIO/dagflat.pm \
2852
Bio/SeqIO/pir.pm \
2853
$(INST_LIB)/Bio/SeqIO/pir.pm \
2854
Bio/Factory/SequenceStreamI.pm \
2855
$(INST_LIB)/Bio/Factory/SequenceStreamI.pm \
2856
Bio/Annotation/Comment.pm \
2857
$(INST_LIB)/Bio/Annotation/Comment.pm \
2858
Bio/Matrix/PhylipDist.pm \
2859
$(INST_LIB)/Bio/Matrix/PhylipDist.pm \
2860
Bio/Tools/BPlite.pm \
2861
$(INST_LIB)/Bio/Tools/BPlite.pm \
2862
Bio/Tools/Genewise.pm \
2863
$(INST_LIB)/Bio/Tools/Genewise.pm \
2864
Bio/Symbol/ProteinAlphabet.pm \
2865
$(INST_LIB)/Bio/Symbol/ProteinAlphabet.pm \
2866
Bio/Biblio/PubmedArticle.pm \
2867
$(INST_LIB)/Bio/Biblio/PubmedArticle.pm \
2868
Bio/Perl.pm \
2869
$(INST_LIB)/Bio/Perl.pm \
2870
Bio/Search/HSP/HSPI.pm \
2871
$(INST_LIB)/Bio/Search/HSP/HSPI.pm \
2872
Bio/LiveSeq/Exon.pm \
2873
$(INST_LIB)/Bio/LiveSeq/Exon.pm \
2874
Bio/SeqIO/game/gameHandler.pm \
2875
$(INST_LIB)/Bio/SeqIO/game/gameHandler.pm \
2876
Bio/LiveSeq/Chain.pm \
2877
$(INST_LIB)/Bio/LiveSeq/Chain.pm \
2878
Bio/ClusterIO/dbsnp.pm \
2879
$(INST_LIB)/Bio/ClusterIO/dbsnp.pm \
2880
Bio/SearchIO/IteratedSearchResultEventBuilder.pm \
2881
$(INST_LIB)/Bio/SearchIO/IteratedSearchResultEventBuilder.pm \
2882
Bio/Root/Xref.pm \
2883
$(INST_LIB)/Bio/Root/Xref.pm \
2884
Bio/Tools/Run/WrapperBase.pm \
2885
$(INST_LIB)/Bio/Tools/Run/WrapperBase.pm \
2886
Bio/AlignIO/meme.pm \
2887
$(INST_LIB)/Bio/AlignIO/meme.pm \
2888
Bio/Map/MapI.pm \
2889
$(INST_LIB)/Bio/Map/MapI.pm \
2890
Bio/Tools/Genomewise.pm \
2891
$(INST_LIB)/Bio/Tools/Genomewise.pm \
2892
Bio/Location/WidestCoordPolicy.pm \
2893
$(INST_LIB)/Bio/Location/WidestCoordPolicy.pm \
2894
Bio/PopGen/Marker.pm \
2895
$(INST_LIB)/Bio/PopGen/Marker.pm \
2896
Bio/DB/Flat/BDB/embl.pm \
2897
$(INST_LIB)/Bio/DB/Flat/BDB/embl.pm \
2898
Bio/Search/HSP/BlastHSP.pm \
2899
$(INST_LIB)/Bio/Search/HSP/BlastHSP.pm \
2900
Bio/LiveSeq/Mutator.pm \
2901
$(INST_LIB)/Bio/LiveSeq/Mutator.pm \
2902
Bio/Tools/Eponine.pm \
2903
$(INST_LIB)/Bio/Tools/Eponine.pm \
2904
Bio/SeqFeature/Gene/Intron.pm \
2905
$(INST_LIB)/Bio/SeqFeature/Gene/Intron.pm \
2906
Bio/DB/GFF/RelSegment.pm \
2907
$(INST_LIB)/Bio/DB/GFF/RelSegment.pm \
2908
Bio/Phenotype/Measure.pm \
2909
$(INST_LIB)/Bio/Phenotype/Measure.pm \
2910
Bio/DB/GFF/Aggregator/ucsc_ensgene.pm \
2911
$(INST_LIB)/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm \
2912
Bio/Annotation/TypeManager.pm \
2913
$(INST_LIB)/Bio/Annotation/TypeManager.pm \
2914
Bio/Map/OrderedPosition.pm \
2915
$(INST_LIB)/Bio/Map/OrderedPosition.pm \
2916
Bio/SeqIO/MultiFile.pm \
2917
$(INST_LIB)/Bio/SeqIO/MultiFile.pm \
2918
Bio/Tools/Tmhmm.pm \
2919
$(INST_LIB)/Bio/Tools/Tmhmm.pm \
2920
Bio/Factory/SeqAnalysisParserFactory.pm \
2921
$(INST_LIB)/Bio/Factory/SeqAnalysisParserFactory.pm \
2922
Bio/SeqFeature/Gene/UTR.pm \
2923
$(INST_LIB)/Bio/SeqFeature/Gene/UTR.pm \
2924
Bio/AlignIO/selex.pm \
2925
$(INST_LIB)/Bio/AlignIO/selex.pm \
2926
Bio/Map/CytoMarker.pm \
2927
$(INST_LIB)/Bio/Map/CytoMarker.pm \
2928
Bio/Seq/SeqBuilder.pm \
2929
$(INST_LIB)/Bio/Seq/SeqBuilder.pm \
2930
Bio/Biblio/Service.pm \
2931
$(INST_LIB)/Bio/Biblio/Service.pm \
2932
Bio/Biblio/MedlineJournal.pm \
2933
$(INST_LIB)/Bio/Biblio/MedlineJournal.pm \
2934
Bio/DB/GenPept.pm \
2935
$(INST_LIB)/Bio/DB/GenPept.pm \
2936
Bio/SeqIO/game/featHandler.pm \
2937
$(INST_LIB)/Bio/SeqIO/game/featHandler.pm \
2938
Bio/Index/Blast.pm \
2939
$(INST_LIB)/Bio/Index/Blast.pm \
2940
Bio/Search/DatabaseI.pm \
2941
$(INST_LIB)/Bio/Search/DatabaseI.pm \
2942
Bio/Tools/Blat.pm \
2943
$(INST_LIB)/Bio/Tools/Blat.pm \
2944
Bio/Graphics/Glyph.pm \
2945
$(INST_LIB)/Bio/Graphics/Glyph.pm \
2946
Bio/Symbol/SymbolI.pm \
2947
$(INST_LIB)/Bio/Symbol/SymbolI.pm \
2948
Bio/Tools/EPCR.pm \
2949
$(INST_LIB)/Bio/Tools/EPCR.pm \
2950
Bio/Tools/pSW.pm \
2951
$(INST_LIB)/Bio/Tools/pSW.pm \
2952
Bio/Location/NarrowestCoordPolicy.pm \
2953
$(INST_LIB)/Bio/Location/NarrowestCoordPolicy.pm \
2954
Bio/AnnotatableI.pm \
2955
$(INST_LIB)/Bio/AnnotatableI.pm \
2956
Bio/Biblio/Proceeding.pm \
2957
$(INST_LIB)/Bio/Biblio/Proceeding.pm \
2958
Bio/TreeIO/newick.pm \
2959
$(INST_LIB)/Bio/TreeIO/newick.pm \
2960
Bio/SeqFeature/Gene/GeneStructure.pm \
2961
$(INST_LIB)/Bio/SeqFeature/Gene/GeneStructure.pm \
2962
Bio/Biblio/Book.pm \
2963
$(INST_LIB)/Bio/Biblio/Book.pm \
2964
Bio/Tree/Statistics.pm \
2965
$(INST_LIB)/Bio/Tree/Statistics.pm \
2966
Bio/Tools/BPlite/Iteration.pm \
2967
$(INST_LIB)/Bio/Tools/BPlite/Iteration.pm \
2968
Bio/SearchIO/Writer/HTMLResultWriter.pm \
2969
$(INST_LIB)/Bio/SearchIO/Writer/HTMLResultWriter.pm \
2970
Bio/Align/PairwiseStatistics.pm \
2971
$(INST_LIB)/Bio/Align/PairwiseStatistics.pm \
2972
Bio/Assembly/IO.pm \
2973
$(INST_LIB)/Bio/Assembly/IO.pm \
2974
Bio/Graphics/Glyph/span.pm \
2975
$(INST_LIB)/Bio/Graphics/Glyph/span.pm \
2976
Bio/Ontology/TermFactory.pm \
2977
$(INST_LIB)/Bio/Ontology/TermFactory.pm \
2978
Bio/Tools/SeqWords.pm \
2979
$(INST_LIB)/Bio/Tools/SeqWords.pm \
2980
Bio/DB/GFF/Adaptor/dbi/oracleace.pm \
2981
$(INST_LIB)/Bio/DB/GFF/Adaptor/dbi/oracleace.pm \
2982
Bio/Expression/FeatureI.pm \
2983
$(INST_LIB)/Bio/Expression/FeatureI.pm \
2984
Bio/Map/OrderedPositionWithDistance.pm \
2985
$(INST_LIB)/Bio/Map/OrderedPositionWithDistance.pm \
2986
Bio/SeqIO/game.pm \
2987
$(INST_LIB)/Bio/SeqIO/game.pm \
2988
Bio/Biblio/IO/pubmed2ref.pm \
2989
$(INST_LIB)/Bio/Biblio/IO/pubmed2ref.pm \
2990
Bio/Index/Abstract.pm \
2991
$(INST_LIB)/Bio/Index/Abstract.pm \
2992
Bio/Tools/HMMER/Domain.pm \
2993
$(INST_LIB)/Bio/Tools/HMMER/Domain.pm \
2994
Bio/Search/Iteration/IterationI.pm \
2995
$(INST_LIB)/Bio/Search/Iteration/IterationI.pm \
2996
Bio/SearchIO/blastxml.pm \
2997
$(INST_LIB)/Bio/SearchIO/blastxml.pm \
2998
Bio/DB/GFF/Adaptor/dbi/oracle.pm \
2999
$(INST_LIB)/Bio/DB/GFF/Adaptor/dbi/oracle.pm \
3000
Bio/Biblio/IO/medlinexml.pm \
3001
$(INST_LIB)/Bio/Biblio/IO/medlinexml.pm \
3002
Bio/Coordinate/GeneMapper.pm \
3003
$(INST_LIB)/Bio/Coordinate/GeneMapper.pm \
3004
Bio/SeqIO/ace.pm \
3005
$(INST_LIB)/Bio/SeqIO/ace.pm \
3006
Bio/Location/FuzzyLocationI.pm \
3007
$(INST_LIB)/Bio/Location/FuzzyLocationI.pm \
3008
Bio/Search/Hit/Fasta.pm \
3009
$(INST_LIB)/Bio/Search/Hit/Fasta.pm \
3010
Bio/Root/Exception.pm \
3011
$(INST_LIB)/Bio/Root/Exception.pm \
3012
Bio/Factory/TreeFactoryI.pm \
3013
$(INST_LIB)/Bio/Factory/TreeFactoryI.pm \
3014
Bio/Assembly/IO/ace.pm \
3015
$(INST_LIB)/Bio/Assembly/IO/ace.pm \
3016
Bio/DB/Biblio/soap.pm \
3017
$(INST_LIB)/Bio/DB/Biblio/soap.pm \
3018
Bio/SeqIO/tab.pm \
3019
$(INST_LIB)/Bio/SeqIO/tab.pm \
3020
Bio/Root/Object.pm \
3021
$(INST_LIB)/Bio/Root/Object.pm
3022
3023
3024
# --- MakeMaker platform_constants section:
3025
MM_Unix_VERSION = 1.42
3026
PERL_MALLOC_DEF = -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc
3027
3028
3029
# --- MakeMaker tool_autosplit section:
3030
# Usage: $(AUTOSPLITFILE) FileToSplit AutoDirToSplitInto
3031
AUTOSPLITFILE = $(PERLRUN) -e 'use AutoSplit; autosplit($$ARGV[0], $$ARGV[1], 0, 1, 1)'
3032
3033
3034
3035
# --- MakeMaker tool_xsubpp section:
3036
3037
3038
# --- MakeMaker tools_other section:
3039
SHELL = /bin/sh
3040
CHMOD = chmod
3041
CP = cp
3042
MV = mv
3043
NOOP = $(SHELL) -c true
3044
NOECHO = @
3045
RM_F = rm -f
3046
RM_RF = rm -rf
3047
TEST_F = test -f
3048
TOUCH = touch
3049
UMASK_NULL = umask 0
3050
DEV_NULL = > /dev/null 2>&1
3051
MKPATH = $(PERLRUN) "-MExtUtils::Command" -e mkpath
3052
EQUALIZE_TIMESTAMP = $(PERLRUN) "-MExtUtils::Command" -e eqtime
3053
ECHO = echo
3054
ECHO_N = echo -n
3055
UNINST = 0
3056
VERBINST = 0
3057
MOD_INSTALL = $(PERLRUN) -MExtUtils::Install -e 'install({@ARGV}, '\''$(VERBINST)'\'', 0, '\''$(UNINST)'\'');'
3058
DOC_INSTALL = $(PERLRUN) "-MExtUtils::Command::MM" -e perllocal_install
3059
UNINSTALL = $(PERLRUN) "-MExtUtils::Command::MM" -e uninstall
3060
WARN_IF_OLD_PACKLIST = $(PERLRUN) "-MExtUtils::Command::MM" -e warn_if_old_packlist
3061
3062
3063
# --- MakeMaker makemakerdflt section:
3064
makemakerdflt: all
3065
$(NOECHO) $(NOOP)
3066
3067
3068
# --- MakeMaker dist section:
3069
TAR = tar
3070
TARFLAGS = cvf
3071
ZIP = zip
3072
ZIPFLAGS = -r
3073
COMPRESS = gzip -9f
3074
SUFFIX = .gz
3075
SHAR = shar
3076
PREOP = $(NOECHO) $(NOOP)
3077
POSTOP = $(NOECHO) $(NOOP)
3078
TO_UNIX = $(NOECHO) $(NOOP)
3079
CI = ci -u
3080
RCS_LABEL = rcs -Nv$(VERSION_SYM): -q
3081
DIST_CP = best
3082
DIST_DEFAULT = all tardist
3083
DISTNAME = bioperl
3084
DISTVNAME = bioperl-1.4
3085
3086
3087
# --- MakeMaker macro section:
3088
3089
3090
# --- MakeMaker depend section:
3091
3092
3093
# --- MakeMaker cflags section:
3094
3095
3096
# --- MakeMaker const_loadlibs section:
3097
3098
3099
# --- MakeMaker const_cccmd section:
3100
3101
3102
# --- MakeMaker post_constants section:
3103
3104
3105
# --- MakeMaker pasthru section:
3106
3107
PASTHRU = LIB="$(LIB)"\
3108
LIBPERL_A="$(LIBPERL_A)"\
3109
LINKTYPE="$(LINKTYPE)"\
3110
PREFIX="$(PREFIX)"\
3111
OPTIMIZE="$(OPTIMIZE)"\
3112
PASTHRU_DEFINE="$(PASTHRU_DEFINE)"\
3113
PASTHRU_INC="$(PASTHRU_INC)"
3114
3115
3116
# --- MakeMaker special_targets section:
3117
.SUFFIXES: .xs .c .C .cpp .i .s .cxx .cc $(OBJ_EXT)
3118
3119
.PHONY: all config static dynamic test linkext manifest
3120
3121
3122
3123
# --- MakeMaker c_o section:
3124
3125
3126
# --- MakeMaker xs_c section:
3127
3128
3129
# --- MakeMaker xs_o section:
3130
3131
3132
# --- MakeMaker top_targets section:
3133
all :: pure_all manifypods
3134
$(NOECHO) $(NOOP)
3135
3136
3137
pure_all :: config pm_to_blib subdirs linkext
3138
$(NOECHO) $(NOOP)
3139
3140
subdirs :: $(MYEXTLIB)
3141
$(NOECHO) $(NOOP)
3142
3143
config :: $(FIRST_MAKEFILE) $(INST_LIBDIR)$(DIRFILESEP).exists
3144
$(NOECHO) $(NOOP)
3145
3146
config :: $(INST_ARCHAUTODIR)$(DIRFILESEP).exists
3147
$(NOECHO) $(NOOP)
3148
3149
config :: $(INST_AUTODIR)$(DIRFILESEP).exists
3150
$(NOECHO) $(NOOP)
3151
3152
$(INST_AUTODIR)/.exists :: /usr/lib/perl5/5.8.2/i386-linux-thread-multi/CORE/perl.h
3153
$(NOECHO) $(MKPATH) $(INST_AUTODIR)
3154
$(NOECHO) $(EQUALIZE_TIMESTAMP) /usr/lib/perl5/5.8.2/i386-linux-thread-multi/CORE/perl.h $(INST_AUTODIR)/.exists
3155
3156
-$(NOECHO) $(CHMOD) $(PERM_RWX) $(INST_AUTODIR)
3157
3158
$(INST_LIBDIR)/.exists :: /usr/lib/perl5/5.8.2/i386-linux-thread-multi/CORE/perl.h
3159
$(NOECHO) $(MKPATH) $(INST_LIBDIR)
3160
$(NOECHO) $(EQUALIZE_TIMESTAMP) /usr/lib/perl5/5.8.2/i386-linux-thread-multi/CORE/perl.h $(INST_LIBDIR)/.exists
3161
3162
-$(NOECHO) $(CHMOD) $(PERM_RWX) $(INST_LIBDIR)
3163
3164
$(INST_ARCHAUTODIR)/.exists :: /usr/lib/perl5/5.8.2/i386-linux-thread-multi/CORE/perl.h
3165
$(NOECHO) $(MKPATH) $(INST_ARCHAUTODIR)
3166
$(NOECHO) $(EQUALIZE_TIMESTAMP) /usr/lib/perl5/5.8.2/i386-linux-thread-multi/CORE/perl.h $(INST_ARCHAUTODIR)/.exists
3167
3168
-$(NOECHO) $(CHMOD) $(PERM_RWX) $(INST_ARCHAUTODIR)
3169
3170
config :: $(INST_MAN3DIR)$(DIRFILESEP).exists
3171
$(NOECHO) $(NOOP)
3172
3173
3174
$(INST_MAN3DIR)/.exists :: /usr/lib/perl5/5.8.2/i386-linux-thread-multi/CORE/perl.h
3175
$(NOECHO) $(MKPATH) $(INST_MAN3DIR)
3176
$(NOECHO) $(EQUALIZE_TIMESTAMP) /usr/lib/perl5/5.8.2/i386-linux-thread-multi/CORE/perl.h $(INST_MAN3DIR)/.exists
3177
3178
-$(NOECHO) $(CHMOD) $(PERM_RWX) $(INST_MAN3DIR)
3179
3180
help:
3181
perldoc ExtUtils::MakeMaker
3182
3183
3184
# --- MakeMaker linkext section:
3185
3186
linkext :: $(LINKTYPE)
3187
$(NOECHO) $(NOOP)
3188
3189
3190
# --- MakeMaker dlsyms section:
3191
3192
3193
# --- MakeMaker dynamic section:
3194
3195
dynamic :: $(FIRST_MAKEFILE) $(INST_DYNAMIC) $(INST_BOOT)
3196
$(NOECHO) $(NOOP)
3197
3198
3199
# --- MakeMaker dynamic_bs section:
3200
3201
BOOTSTRAP =
3202
3203
3204
# --- MakeMaker dynamic_lib section:
3205
3206
3207
# --- MakeMaker static section:
3208
3209
## $(INST_PM) has been moved to the all: target.
3210
## It remains here for awhile to allow for old usage: "make static"
3211
static :: $(FIRST_MAKEFILE) $(INST_STATIC)
3212
$(NOECHO) $(NOOP)
3213
3214
3215
# --- MakeMaker static_lib section:
3216
3217
3218
# --- MakeMaker manifypods section:
3219
3220
manifypods : pure_all
3221
@$(NOOP)
3222
3223
3224
# --- MakeMaker processPL section:
3225
3226
all :: bioscripts.pod
3227
$(NOECHO) $(NOOP)
3228
3229
bioscripts.pod :: doc/makedoc.PL
3230
$(PERLRUNINST) doc/makedoc.PL bioscripts.pod
3231
3232
all :: biodatabases.pod
3233
$(NOECHO) $(NOOP)
3234
3235
biodatabases.pod :: doc/makedoc.PL
3236
$(PERLRUNINST) doc/makedoc.PL biodatabases.pod
3237
3238
all :: biodesign.pod
3239
$(NOECHO) $(NOOP)
3240
3241
biodesign.pod :: doc/makedoc.PL
3242
$(PERLRUNINST) doc/makedoc.PL biodesign.pod
3243
3244
all :: bioperl.pod
3245
$(NOECHO) $(NOOP)
3246
3247
bioperl.pod :: doc/makedoc.PL
3248
$(PERLRUNINST) doc/makedoc.PL bioperl.pod
3249
3250
3251
# --- MakeMaker installbin section:
3252
3253
3254
# --- MakeMaker subdirs section:
3255
3256
# none
3257
3258
# --- MakeMaker clean_subdirs section:
3259
clean_subdirs :
3260
$(NOECHO) $(NOOP)
3261
3262
3263
# --- MakeMaker clean section:
3264
3265
# Delete temporary files but do not touch installed files. We don't delete
3266
# the Makefile here so a later make realclean still has a makefile to use.
3267
3268
clean :: clean_subdirs
3269
-$(RM_RF) ./blib $(MAKE_APERL_FILE) $(INST_ARCHAUTODIR)/extralibs.all $(INST_ARCHAUTODIR)/extralibs.ld perlmain.c tmon.out mon.out so_locations pm_to_blib *$(OBJ_EXT) *$(LIB_EXT) perl.exe perl perl$(EXE_EXT) $(BOOTSTRAP) $(BASEEXT).bso $(BASEEXT).def lib$(BASEEXT).def $(BASEEXT).exp $(BASEEXT).x core core.*perl.*.? *perl.core core.[0-9] core.[0-9][0-9] core.[0-9][0-9][0-9] core.[0-9][0-9][0-9][0-9] core.[0-9][0-9][0-9][0-9][0-9]
3270
-$(MV) $(FIRST_MAKEFILE) $(MAKEFILE_OLD) $(DEV_NULL)
3271
-rm -rf scripts_temp
3272
3273
3274
# --- MakeMaker realclean_subdirs section:
3275
realclean_subdirs :
3276
$(NOECHO) $(NOOP)
3277
3278
3279
# --- MakeMaker realclean section:
3280
3281
# Delete temporary files (via clean) and also delete installed files
3282
realclean purge :: clean realclean_subdirs
3283
$(RM_RF) $(INST_AUTODIR) $(INST_ARCHAUTODIR)
3284
$(RM_RF) $(DISTVNAME)
3285
$(RM_F) $(INST_LIB)/Bio/AlignIO/maf.pm $(INST_LIB)/Bio/MapIO/mapmaker.pm $(INST_LIB)/Bio/Index/AbstractSeq.pm $(INST_LIB)/Bio/Phenotype/OMIM/OMIMentry.pm $(INST_LIB)/Bio/Tools/HMMER/Set.pm
3286
$(RM_F) $(INST_LIB)/Bio/LiveSeq/Exon.pm $(INST_LIB)/Bio/Search/Iteration/GenericIteration.pm $(INST_LIB)/Bio/Tools/CodonTable.pm $(INST_LIB)/Bio/Tools/Sigcleave.pm
3287
$(RM_F) $(INST_LIB)/Bio/SeqFeature/Tools/TypeMapper.pm $(INST_LIB)/Bio/Biblio/MedlineArticle.pm $(INST_LIB)/Bio/SeqIO/FTHelper.pm $(INST_LIB)/Bio/Ontology/Path.pm $(INST_LIB)/Bio/Ontology/Ontology.pm
3288
$(RM_F) $(INST_LIB)/Bio/Seq/LargeSeq.pm $(INST_LIB)/Bio/Search/HSP/HSPFactory.pm $(INST_LIB)/Bio/Annotation/SimpleValue.pm $(INST_LIB)/Bio/SeqIO/swiss.pm $(INST_LIB)/Bio/Tools/BPlite.pm
3289
$(RM_F) $(INST_LIB)/Bio/Variation/DNAMutation.pm $(INST_LIB)/Bio/Range.pm $(INST_LIB)/Bio/Factory/HitFactoryI.pm $(INST_LIB)/Bio/Tools/GuessSeqFormat.pm $(INST_LIB)/Bio/Graphics/Glyph/dna.pm
3290
$(RM_F) $(INST_LIB)/Bio/Assembly/IO/phrap.pm $(INST_LIB)/Bio/Biblio/BookArticle.pm $(INST_LIB)/Bio/DB/GFF/Aggregator/coding.pm $(INST_LIB)/Bio/Structure/SecStr/STRIDE/Res.pm
3291
$(RM_F) $(INST_LIB)/Bio/SearchIO/Writer/ResultTableWriter.pm $(INST_LIB)/Bio/OntologyIO/InterProParser.pm $(INST_LIB)/Bio/Das/FeatureTypeI.pm $(INST_LIB)/Bio/Seq/PrimedSeq.pm
3292
$(RM_F) $(INST_LIB)/Bio/Expression/FeatureI.pm $(INST_LIB)/Bio/Graphics/Glyph/anchored_arrow.pm $(INST_LIB)/Bio/Root/Object.pm $(INST_LIB)/Bio/Seq/LargePrimarySeq.pm $(INST_LIB)/Bio/AlignIO/bl2seq.pm
3293
$(RM_F) $(INST_LIB)/Bio/Tools/ESTScan.pm $(INST_LIB)/Bio/PopGen/IO/prettybase.pm $(INST_LIB)/Bio/Tools/Primer/Assessor/Base.pm $(INST_LIB)/Bio/DB/Flat/BDB/embl.pm $(INST_LIB)/Bio/Tools/Profile.pm
3294
$(RM_F) $(INST_LIB)/Bio/DB/QueryI.pm $(INST_LIB)/Bio/Graphics/Glyph/splice_site.pm $(INST_LIB)/Bio/Root/Version.pm $(INST_LIB)/Bio/DB/RefSeq.pm $(INST_LIB)/Bio/Matrix/IO.pm
3295
$(RM_F) $(INST_LIB)/Bio/PopGen/Simulation/GeneticDrift.pm $(INST_LIB)/Bio/Tools/Phylo/Phylip/ProtDist.pm $(INST_LIB)/Bio/Matrix/Generic.pm $(INST_LIB)/Bio/Graphics/Glyph/extending_arrow.pm
3296
$(RM_F) $(INST_LIB)/Bio/Ontology/InterProTerm.pm $(INST_LIB)/Bio/Tools/SeqStats.pm $(INST_LIB)/Bio/Factory/LocationFactoryI.pm $(INST_LIB)/Bio/Search/HSP/PSLHSP.pm $(INST_LIB)/Bio/DB/Universal.pm
3297
$(RM_F) $(INST_LIB)/Bio/Map/SimpleMap.pm $(INST_LIB)/Bio/SeqIO/metafasta.pm $(INST_LIB)/Bio/Map/MarkerI.pm $(INST_LIB)/Bio/Tools/Analysis/Protein/ELM.pm $(INST_LIB)/Bio/Graphics/Glyph.pm
3298
$(RM_F) $(INST_LIB)/Bio/Tree/AlleleNode.pm $(INST_LIB)/Bio/Tools/Run/WrapperBase.pm $(INST_LIB)/Bio/Variation/SNP.pm $(INST_LIB)/Bio/Graphics/Glyph/cds.pm $(INST_LIB)/Bio/CodonUsage/Table.pm
3299
$(RM_F) $(INST_LIB)/Bio/DB/GFF/Adaptor/biofetch_oracle.pm $(INST_LIB)/Bio/SearchIO/axt.pm $(INST_LIB)/Bio/Tools/Blat.pm $(INST_LIB)/Bio/Tools/BPlite/HSP.pm $(INST_LIB)/Bio/Map/CytoMap.pm
3300
$(RM_F) $(INST_LIB)/Bio/Coordinate/ResultI.pm $(INST_LIB)/Bio/SeqFeature/Collection.pm $(INST_LIB)/Bio/Phenotype/MeSH/Twig.pm $(INST_LIB)/Bio/SeqIO/raw.pm $(INST_LIB)/Bio/Factory/SeqAnalysisParserFactoryI.pm
3301
$(RM_F) $(INST_LIB)/Bio/Search/GenericDatabase.pm $(INST_LIB)/Bio/Location/WidestCoordPolicy.pm $(INST_LIB)/Bio/AlignIO/phylip.pm $(INST_LIB)/Bio/Search/HSP/HMMERHSP.pm
3302
$(RM_F) $(INST_LIB)/Bio/SearchIO/Writer/GbrowseGFF.pm $(INST_LIB)/Bio/SearchIO/megablast.pm $(INST_LIB)/Bio/Graphics/Glyph/xyplot.pm $(INST_LIB)/Bio/PopGen/Simulation/Coalescent.pm
3303
$(RM_F) $(INST_LIB)/Bio/Location/Split.pm $(INST_LIB)/biodatabases.pod $(INST_LIB)/Bio/SeqUtils.pm $(INST_LIB)/Bio/Tools/Primer3.pm $(INST_LIB)/bioperl.pod $(INST_LIB)/Bio/SeqFeature/Primer.pm
3304
$(RM_F) $(INST_LIB)/Bio/Structure/IO/pdb.pm $(INST_LIB)/Bio/Variation/VariantI.pm $(INST_LIB)/Bio/Tools/SeqAnal.pm $(INST_LIB)/Bio/Tools/Analysis/SimpleAnalysisBase.pm $(INST_LIB)/Bio/Cluster/FamilyI.pm
3305
$(RM_F) $(INST_LIB)/Bio/Biblio/Person.pm $(INST_LIB)/Bio/Matrix/PSM/PsmHeader.pm $(INST_LIB)/Bio/Map/Position.pm $(INST_LIB)/Bio/SeqIO/game/gameWriter.pm $(INST_LIB)/Bio/CodonUsage/IO.pm
3306
$(RM_F) $(INST_LIB)/Bio/SeqIO/fastq.pm $(INST_LIB)/Bio/SeqFeature/SiRNA/Pair.pm $(INST_LIB)/Bio/Tools/Grail.pm $(INST_LIB)/Bio/Variation/AAChange.pm $(INST_LIB)/Bio/Graphics/Glyph/transcript2.pm
3307
$(RM_F) $(INST_LIB)/Bio/Tools/Blast/Sbjct.pm $(INST_LIB)/Bio/DB/Taxonomy.pm $(INST_LIB)/Bio/Structure/Model.pm $(INST_LIB)/Bio/Annotation/Comment.pm $(INST_LIB)/Bio/ClusterIO/dbsnp.pm
3308
$(RM_F) $(INST_LIB)/Bio/SeqIO/ztr.pm $(INST_LIB)/Bio/SearchIO/Writer/HTMLResultWriter.pm $(INST_LIB)/Bio/Biblio/MedlineJournal.pm $(INST_LIB)/Bio/Taxonomy/FactoryI.pm $(INST_LIB)/Bio/Species.pm
3309
$(RM_F) $(INST_LIB)/Bio/Coordinate/ExtrapolatingPair.pm $(INST_LIB)/Bio/Tools/Eponine.pm $(INST_LIB)/Bio/DB/GFF/Aggregator.pm $(INST_LIB)/Bio/DB/GFF.pm $(INST_LIB)/Bio/SearchIO/blast.pm
3310
$(RM_F) $(INST_LIB)/Bio/Coordinate/Pair.pm $(INST_LIB)/Bio/DB/GFF/Aggregator/alignment.pm $(INST_LIB)/Bio/Tools/EMBOSS/Palindrome.pm $(INST_LIB)/Bio/Annotation/DBLink.pm $(INST_LIB)/Bio/Seq/PrimaryQual.pm
3311
$(RM_F) $(INST_LIB)/Bio/SeqIO/locuslink.pm $(INST_LIB)/Bio/Tools/dpAlign.pm $(INST_LIB)/Bio/Graphics/FeatureFile.pm $(INST_LIB)/Bio/Search/HSP/GenericHSP.pm $(INST_LIB)/Bio/Graphics/Glyph/segmented_keyglyph.pm
3312
$(RM_F) $(INST_LIB)/Bio/Tools/Phylo/PAML/Result.pm $(INST_LIB)/Bio/Coordinate/Utils.pm $(INST_LIB)/Bio/SeqFeature/SiRNA/Oligo.pm $(INST_LIB)/Bio/SeqFeature/Gene/NC_Feature.pm
3313
$(RM_F) $(INST_LIB)/Bio/Restriction/IO/base.pm $(INST_LIB)/Bio/SeqIO/MultiFile.pm $(INST_LIB)/Bio/Ontology/SimpleOntologyEngine.pm $(FIRST_MAKEFILE) $(INST_LIB)/Bio/Index/Fastq.pm
3314
$(RM_F) $(INST_LIB)/Bio/Assembly/ScaffoldI.pm $(INST_LIB)/Bio/Graphics/Glyph/ruler_arrow.pm $(INST_LIB)/Bio/SeqIO/phd.pm $(INST_LIB)/Bio/Cluster/SequenceFamily.pm $(INST_LIB)/Bio/DasI.pm
3315
$(RM_F) $(INST_LIB)/Bio/AlignIO/mega.pm $(INST_LIB)/Bio/DB/GFF/Feature.pm $(INST_LIB)/Bio/Coordinate/Result/Gap.pm $(INST_LIB)/Bio/RangeI.pm $(INST_LIB)/Bio/Tools/EPCR.pm $(INST_LIB)/Bio/Tools/Tmhmm.pm
3316
$(RM_F) $(INST_LIB)/Bio/Graphics/Glyph/Factory.pm $(INST_LIB)/Bio/DB/GFF/Adaptor/memory_iterator.pm $(INST_LIB)/Bio/Biblio/Proceeding.pm $(INST_LIB)/Bio/Graphics/Glyph/graded_segments.pm
3317
$(RM_F) $(INST_LIB)/Bio/Variation/README $(INST_LIB)/Bio/Tools/Promoterwise.pm $(INST_LIB)/Bio/Graphics/Feature.pm $(INST_LIB)/Bio/AlignIO/metafasta.pm $(INST_LIB)/Bio/Tools/Blast.pm
3318
$(RM_F) $(INST_LIB)/Bio/SeqIO/ace.pm $(INST_LIB)/Bio/Biblio/Book.pm $(INST_LIB)/Bio/Biblio/Provider.pm $(INST_LIB)/Bio/Biblio/WebResource.pm $(INST_LIB)/Bio/Search/Hit/Fasta.pm
3319
$(RM_F) $(INST_LIB)/Bio/Tools/BPlite/Iteration.pm $(INST_LIB)/Bio/SeqFeature/PositionProxy.pm $(INST_LIB)/Bio/Ontology/RelationshipI.pm $(INST_LIB)/Bio/Matrix/PSM/IO.pm $(INST_LIB)/Bio/Structure/IO.pm
3320
$(RM_F) $(INST_LIB)/Bio/AnalysisParserI.pm $(INST_LIB)/Bio/DB/Taxonomy/flatfile.pm $(INST_LIB)/Bio/SearchIO/wise.pm $(INST_LIB)/Bio/Graphics/Glyph/span.pm $(INST_LIB)/Bio/Structure/Residue.pm
3321
$(RM_F) $(INST_LIB)/Bio/DB/GDB.pm $(INST_LIB)/Bio/SeqIO/genbank.pm $(INST_LIB)/Bio/LocationI.pm $(INST_LIB)/Bio/Tools/BPlite/Sbjct.pm $(INST_LIB)/Bio/Root/IO.pm $(INST_LIB)/Bio/SeqIO.pm
3322
$(RM_F) $(INST_LIB)/Bio/Search/Hit/HitI.pm $(INST_LIB)/Bio/LiveSeq/SeqI.pm $(INST_LIB)/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm $(INST_LIB)/Bio/PopGen/Statistics.pm
3323
$(RM_F) $(INST_LIB)/Bio/SearchIO/FastHitEventBuilder.pm $(INST_LIB)/Bio/DB/GFF/Adaptor/dbi/mysql.pm $(INST_LIB)/Bio/Matrix/PhylipDist.pm $(INST_LIB)/Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm
3324
$(RM_F) $(INST_LIB)/Bio/DB/Flat/BDB/swissprot.pm $(INST_LIB)/Bio/Cluster/UniGeneI.pm $(INST_LIB)/Bio/Root/Vector.pm $(INST_LIB)/Bio/DB/GFF/Aggregator/processed_transcript.pm $(INST_LIB)/Bio/Tools/Geneid.pm
3325
$(RM_F) $(INST_LIB)/biodesign.pod $(INST_LIB)/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm $(INST_LIB)/Bio/Tree/NodeI.pm $(INST_LIB)/Bio/Graphics/Glyph/segments.pm $(INST_LIB)/Bio/Graphics/Glyph/minmax.pm
3326
$(RM_F) $(INST_LIB)/Bio/Search/Result/BlastResult.pm $(INST_LIB)/Bio/Assembly/IO/ace.pm $(INST_LIB)/Bio/Graphics/Pictogram.pm $(INST_LIB)/Bio/Tools/AnalysisResult.pm $(INST_LIB)/Bio/Tools/Est2Genome.pm
3327
$(RM_F) $(INST_LIB)/Bio/Search/DatabaseI.pm $(INST_LIB)/Bio/Biblio.pm $(INST_LIB)/Bio/DB/GFF/Segment.pm $(INST_LIB)/Bio/Restriction/EnzymeCollection.pm $(INST_LIB)/Bio/DB/BioFetch.pm
3328
$(RM_F) $(INST_LIB)/Bio/Tools/IUPAC.pm $(INST_LIB)/Bio/SeqIO/game/seqHandler.pm $(INST_LIB)/Bio/OntologyIO.pm $(INST_LIB)/Bio/Search/Hit/HMMERHit.pm $(INST_LIB)/Bio/SeqIO/exp.pm
3329
$(RM_F) $(INST_LIB)/Bio/Map/OrderedPositionWithDistance.pm $(INST_LIB)/Bio/Tools/Prints.pm $(INST_LIB)/Bio/Tools/Alignment/Trim.pm $(INST_LIB)/Bio/Tools/WWW.pm $(INST_LIB)/Bio/Annotation/TypeManager.pm
3330
$(RM_F) $(INST_LIB)/Bio/Ontology/TermFactory.pm $(INST_LIB)/Bio/Map/CytoPosition.pm $(INST_LIB)/Bio/TreeIO/newick.pm $(INST_LIB)/Bio/Cluster/UniGene.pm $(INST_LIB)/Bio/SeqAnalysisParserI.pm
3331
$(RM_F) $(INST_LIB)/Bio/SeqFeature/Gene/Poly_A_site.pm $(INST_LIB)/Bio/Graphics.pm $(INST_LIB)/Bio/Factory/ResultFactoryI.pm $(INST_LIB)/Bio/Matrix/PSM/PsmI.pm $(INST_LIB)/Bio/DB/GFF/RelSegment.pm
3332
$(RM_F) $(INST_LIB)/Bio/AnalysisI.pm $(INST_LIB)/Bio/Event/EventHandlerI.pm $(INST_LIB)/Bio/Structure/SecStr/DSSP/Res.pm $(INST_LIB)/Bio/LiveSeq/Range.pm $(INST_LIB)/Bio/MapIO.pm
3333
$(RM_F) $(INST_LIB)/Bio/SeqFeature/Gene/ExonI.pm $(INST_LIB)/Bio/Tree/Node.pm $(INST_LIB)/Bio/TreeIO/lintree.pm $(INST_LIB)/Bio/PopGen/Genotype.pm $(INST_LIB)/Bio/SearchIO/sim4.pm
3334
$(RM_F) $(INST_LIB)/Bio/Expression/FeatureGroup/FeatureGroupMas50.pm $(INST_LIB)/Bio/LiveSeq/ChainI.pm $(INST_LIB)/Bio/Tools/Genscan.pm $(INST_LIB)/Bio/Index/SwissPfam.pm $(INST_LIB)/Bio/Restriction/Enzyme.pm
3335
$(RM_F) $(INST_LIB)/Bio/SeqFeature/SimilarityPair.pm $(INST_LIB)/Bio/Factory/SequenceProcessorI.pm $(INST_LIB)/Bio/DB/Flat/BDB/genbank.pm $(INST_LIB)/Bio/DB/GFF/Featname.pm $(INST_LIB)/Bio/UpdateableSeqI.pm
3336
$(RM_F) $(INST_LIB)/Bio/OntologyIO/simplehierarchy.pm $(INST_LIB)/Bio/Map/Marker.pm $(INST_LIB)/Bio/Biblio/PubmedJournalArticle.pm $(INST_LIB)/Bio/Map/Microsatellite.pm
3337
$(RM_F) $(INST_LIB)/Bio/SeqFeature/Computation.pm $(INST_LIB)/Bio/Taxonomy/Taxon.pm $(INST_LIB)/Bio/AlignIO/nexus.pm $(INST_LIB)/Bio/Search/Result/ResultFactory.pm $(INST_LIB)/Bio/LiveSeq/Chain.pm
3338
$(RM_F) $(INST_LIB)/Bio/Factory/SequenceFactoryI.pm $(INST_LIB)/Bio/Factory/SeqAnalysisParserFactory.pm $(INST_LIB)/Bio/DB/EMBL.pm ./Seq.pm.bak $(INST_LIB)/Bio/DB/GFF/Adaptor/dbi/oracle.pm
3339
$(RM_F) $(INST_LIB)/Bio/Ontology/Relationship.pm $(INST_LIB)/Bio/Tools/HMMER/Results.pm $(INST_LIB)/Bio/Tools/HMMER/Domain.pm $(INST_LIB)/Bio/DB/GFF/Adaptor/dbi/oracleace.pm $(INST_LIB)/Bio/Root/Xref.pm
3340
$(RM_F) $(INST_LIB)/Bio/Restriction/IO/withrefm.pm $(INST_LIB)/Bio/PopGen/Individual.pm $(INST_LIB)/Bio/LocatableSeq.pm $(INST_LIB)/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm
3341
$(RM_F) $(INST_LIB)/Bio/DB/GFF/Aggregator/ucsc_acembly.pm $(INST_LIB)/Bio/Search/Hit/HitFactory.pm $(INST_LIB)/Bio/Graphics/Glyph/processed_transcript.pm $(INST_LIB)/Bio/LiveSeq/Translation.pm
3342
$(RM_F) $(INST_LIB)/Bio/AlignIO/pfam.pm $(INST_LIB)/Bio/Variation/IO.pm $(INST_LIB)/Bio/SimpleAlign.pm $(INST_LIB)/Bio/Annotation/OntologyTerm.pm $(INST_LIB)/Bio/LiveSeq/Repeat_Unit.pm
3343
$(RM_F) $(INST_LIB)/Bio/Tools/RepeatMasker.pm $(INST_LIB)/Bio/Tools/Blast/CHANGES $(INST_LIB)/Bio/Biblio/JournalArticle.pm $(INST_LIB)/Bio/Tools/Analysis/Protein/Mitoprot.pm $(INST_LIB)/Bio/Tools/Coil.pm
3344
$(RM_F) $(INST_LIB)/Bio/SeqIO/game.pm $(INST_LIB)/Bio/Phenotype/Measure.pm $(INST_LIB)/Bio/DB/GFF/Aggregator/none.pm $(INST_LIB)/Bio/SeqIO/gcg.pm $(INST_LIB)/Bio/DB/Query/GenBank.pm
3345
$(RM_F) $(INST_LIB)/Bio/Tools/MZEF.pm $(INST_LIB)/Bio/Graphics/Glyph/crossbox.pm $(INST_LIB)/Bio/PrimarySeq.pm $(INST_LIB)/Bio/Perl.pm $(INST_LIB)/Bio/Restriction/IO.pm $(INST_LIB)/Bio/Tools/Seg.pm
3346
$(RM_F) $(INST_LIB)/Bio/Location/Atomic.pm $(INST_LIB)/Bio/Map/LinkageMap.pm $(INST_LIB)/Bio/Tools/Blast/HTML.pm $(INST_LIB)/Bio/SearchIO/Writer/HSPTableWriter.pm $(INST_LIB)/Bio/Factory/ObjectFactoryI.pm
3347
$(RM_F) $(INST_LIB)/Bio/Matrix/PSM/PsmHeaderI.pm $(INST_LIB)/Bio/Coordinate/Chain.pm $(INST_LIB)/bptutorial.pl $(INST_LIB)/Bio/Biblio/Organisation.pm $(INST_LIB)/Bio/Annotation/AnnotationFactory.pm
3348
$(RM_F) $(INST_LIB)/Bio/SearchIO/blastxml.pm $(INST_LIB)/Bio/Tools/Analysis/DNA/ESEfinder.pm $(INST_LIB)/Bio/Biblio/IO/medline2ref.pm $(INST_LIB)/Bio/SeqFeature/Tools/Unflattener.pm
3349
$(RM_F) $(INST_LIB)/Bio/DB/Flat/BDB.pm $(INST_LIB)/Bio/Biblio/IO/pubmedxml.pm $(INST_LIB)/Bio/Matrix/PSM/IO/mast.pm $(INST_LIB)/Bio/LiveSeq/Repeat_Region.pm $(INST_LIB)/Bio/Graphics/Glyph/diamond.pm
3350
$(RM_F) $(INST_LIB)/Bio/LiveSeq/Gene.pm $(INST_LIB)/Bio/Tools/Prediction/Gene.pm $(INST_LIB)/Bio/AlignIO/fasta.pm $(INST_LIB)/Bio/SearchIO/Writer/BSMLResultWriter.pm $(INST_LIB)/Bio/Matrix/PSM/IO/meme.pm
3351
$(RM_F) $(INST_LIB)/Bio/DB/GenBank.pm $(INST_LIB)/Bio/AlignIO/meme.pm $(INST_LIB)/Bio/Tools/Phylo/Molphy/Result.pm $(INST_LIB)/Bio/Structure/Atom.pm $(INST_LIB)/Bio/Map/MapI.pm
3352
$(RM_F) $(INST_LIB)/Bio/Variation/IO/xml.pm $(INST_LIB)/Bio/Graphics/Glyph/alignment.pm $(INST_LIB)/Bio/DB/Registry.pm $(INST_LIB)/Bio/Seq/SequenceTrace.pm $(INST_LIB)/Bio/LiveSeq/IO/SRS.pm
3353
$(RM_F) $(INST_LIB)/Bio/LiveSeq/AARange.pm $(INST_LIB)/Bio/DB/GFF/Adaptor/dbi/pg.pm $(INST_LIB)/Bio/Align/AlignI.pm $(INST_LIB)/Bio/Biblio/TechReport.pm $(INST_LIB)/Bio/Seq/RichSeq.pm
3354
$(RM_F) $(INST_LIB)/Bio/Tools/Run/StandAloneBlast.pm $(INST_LIB)/Bio/Graphics/Glyph/heterogeneous_segments.pm $(INST_LIB)/Bio/Seq/Meta.pm $(INST_LIB)/Bio/Map/MappableI.pm $(INST_LIB)/Bio/SeqIO/chadoxml.pm
3355
$(RM_F) $(INST_LIB)/Bio/DB/XEMBL.pm $(INST_LIB)/Bio/Index/Swissprot.pm $(INST_LIB)/Bio/Tools/GFF.pm $(INST_LIB)/Bio/DescribableI.pm $(INST_LIB)/Bio/Seq/SeqWithQuality.pm $(INST_LIB)/Bio/SeqIO/largefasta.pm
3356
$(RM_F) $(INST_LIB)/Bio/Tree/RandomFactory.pm $(INST_LIB)/Bio/Factory/ObjectBuilderI.pm $(INST_LIB)/Bio/AlignIO.pm $(INST_LIB)/Bio/PopGen/IndividualI.pm $(INST_LIB)/Bio/Ontology/GOterm.pm
3357
$(RM_F) $(INST_LIB)/Bio/Symbol/DNAAlphabet.pm $(INST_LIB)/Bio/Ontology/SimpleGOEngine.pm $(INST_LIB)/Bio/Tools/Phylo/Molphy.pm $(INST_LIB)/Bio/Tools/Analysis/Protein/Domcut.pm
3358
$(RM_F) $(INST_LIB)/Bio/Factory/ApplicationFactoryI.pm $(INST_LIB)/Bio/LiveSeq/IO/BioPerl.pm $(INST_LIB)/Bio/Ontology/OntologyEngineI.pm $(INST_LIB)/Bio/LiveSeq/Mutator.pm $(INST_LIB)/Bio/Align/StatisticsI.pm
3359
$(RM_F) $(INST_LIB)/Bio/Assembly/ContigAnalysis.pm $(INST_LIB)/Bio/Tools/BPbl2seq.pm $(INST_LIB)/Bio/Factory/TreeFactoryI.pm $(INST_LIB)/Bio/DB/GFF/Adaptor/dbi/iterator.pm $(INST_LIB)/Bio/Search/Processor.pm
3360
$(RM_F) $(INST_LIB)/Bio/Restriction/Analysis.pm $(INST_LIB)/Bio/DB/BiblioI.pm $(INST_LIB)/Bio/Symbol/AlphabetI.pm $(INST_LIB)/Bio/Ontology/Term.pm $(INST_LIB)/Bio/SeqFeatureI.pm
3361
$(RM_F) $(INST_LIB)/Bio/DB/GFF/Aggregator/match.pm $(INST_LIB)/Bio/Search/HSP/BlastHSP.pm $(INST_LIB)/Bio/OntologyIO/soflat.pm $(INST_LIB)/Bio/Factory/AnalysisI.pm $(INST_LIB)/Bio/Tools/Primer/Pair.pm
3362
$(RM_F) $(INST_LIB)/Bio/Search/Result/HMMERResult.pm $(INST_LIB)/Bio/Ontology/OntologyStore.pm $(INST_LIB)/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm $(INST_LIB)/Bio/OntologyIO/Handlers/InterProHandler.pm
3363
$(RM_F) $(INST_LIB)/Bio/Tools/Genomewise.pm $(INST_LIB)/Bio/DB/GFF/Typename.pm $(INST_LIB)/Bio/Biblio/PubmedArticle.pm $(INST_LIB)/Bio/LiveSeq/DNA.pm $(INST_LIB)/Bio/Taxonomy/Tree.pm
3364
$(RM_F) $(INST_LIB)/Bio/Variation/RNAChange.pm $(INST_LIB)/Bio/DB/GFF/Util/Rearrange.pm $(INST_LIB)/Bio/AlignIO/psi.pm $(INST_LIB)/Bio/Map/OrderedPosition.pm $(INST_LIB)/Bio/DB/Makefile.PL
3365
$(RM_F) $(INST_LIB)/Bio/Graphics/FeatureFile/Iterator.pm $(INST_LIB)/Bio/Biblio/IO.pm $(INST_LIB)/Bio/Index/Blast.pm $(INST_LIB)/Bio/DB/RandomAccessI.pm $(INST_LIB)/Bio/SearchIO.pm
3366
$(RM_F) $(INST_LIB)/Bio/Tools/Analysis/Protein/Sopma.pm $(INST_LIB)/Bio/PopGen/Marker.pm $(INST_LIB)/Bio/Biblio/MedlineJournalArticle.pm $(INST_LIB)/Bio/SeqIO/bsml.pm $(INST_LIB)/Bio/DB/FileCache.pm
3367
$(RM_F) $(INST_LIB)/Bio/DBLinkContainerI.pm $(INST_LIB)/Bio/DB/Ace.pm $(INST_LIB)/Bio/DB/Flat/BinarySearch.pm $(INST_LIB)/Bio/Graphics/ConfiguratorI.pm $(INST_LIB)/Bio/Tools/QRNA.pm
3368
$(RM_F) $(INST_LIB)/Bio/SearchIO/waba.pm $(INST_LIB)/Bio/Tools/pICalculator.pm $(INST_LIB)/Bio/Variation/SeqDiff.pm $(INST_LIB)/Bio/Event/EventGeneratorI.pm $(INST_LIB)/Bio/Tree/TreeI.pm
3369
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3370
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3371
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3372
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3373
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3374
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3375
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3376
$(RM_F) $(INST_LIB)/Bio/LiveSeq/Intron.pm $(INST_LIB)/Bio/SeqIO/game/gameHandler.pm $(INST_LIB)/Bio/Coordinate/MapperI.pm $(INST_LIB)/Bio/DB/MANIFEST $(INST_LIB)/Bio/Tools/Signalp.pm
3377
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3378
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3379
$(RM_F) $(INST_LIB)/Bio/AlignIO/emboss.pm $(INST_LIB)/Bio/Tools/Phylo/PAML.pm $(INST_LIB)/Bio/SearchIO/SearchWriterI.pm $(INST_LIB)/Bio/AlignIO/stockholm.pm $(INST_LIB)/Bio/Factory/MapFactoryI.pm
3380
$(RM_F) $(INST_LIB)/Bio/DB/Query/WebQuery.pm $(INST_LIB)/Bio/SeqFeature/Gene/Transcript.pm $(INST_LIB)/Bio/ClusterI.pm $(INST_LIB)/Bio/Graphics/Glyph/toomany.pm $(INST_LIB)/Bio/Tools/ECnumber.pm
3381
$(RM_F) $(INST_LIB)/Bio/DB/WebDBSeqI.pm $(INST_LIB)/Bio/LiveSeq/Mutation.pm $(INST_LIB)/Bio/Index/Abstract.pm $(INST_LIB)/Bio/DB/MeSH.pm $(INST_LIB)/Bio/Search/SearchUtils.pm
3382
$(RM_F) $(INST_LIB)/Bio/SeqFeature/AnnotationAdaptor.pm $(INST_LIB)/Bio/Biblio/MedlineBook.pm $(INST_LIB)/Bio/Graphics/Glyph/transcript.pm $(MAKEFILE_OLD) $(INST_LIB)/Bio/Graphics/Util.pm
3383
$(RM_F) $(INST_LIB)/Bio/Tools/PrositeScan.pm $(INST_LIB)/Bio/Ontology/RelationshipFactory.pm $(INST_LIB)/Bio/SeqFeature/Similarity.pm $(INST_LIB)/Bio/Map/LinkagePosition.pm $(INST_LIB)/Bio/Tools/Lucy.pm
3384
$(RM_F) $(INST_LIB)/Bio/DB/CUTG.pm $(INST_LIB)/Bio/Location/FuzzyLocationI.pm $(INST_LIB)/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm $(INST_LIB)/Bio/Symbol/Symbol.pm $(INST_LIB)/Bio/Ontology/OntologyI.pm
3385
$(RM_F) $(INST_LIB)/Bio/SeqFeature/Gene/Promoter.pm $(INST_LIB)/Bio/SearchDist.pm $(INST_LIB)/Bio/Search/HSP/WABAHSP.pm $(INST_LIB)/Bio/Tools/RandomDistFunctions.pm $(INST_LIB)/Bio/DB/Biblio/soap.pm
3386
$(RM_F) $(INST_LIB)/bioscripts.pod $(INST_LIB)/Bio/Search/Result/GenericResult.pm $(INST_LIB)/Bio/Variation/IO/flat.pm $(INST_LIB)/Bio/Tools/Pseudowise.pm $(INST_LIB)/Bio/SeqIO/tigr.pm
3387
$(RM_F) $(INST_LIB)/Bio/Biblio/PubmedBookArticle.pm $(INST_LIB)/Bio/PopGen/GenotypeI.pm $(INST_LIB)/Bio/Tools/AlignFactory.pm $(INST_LIB)/Bio/DB/XEMBLService.pm $(INST_LIB)/Bio/Search/Result/ResultI.pm
3388
$(RM_F) $(INST_LIB)/Bio/Seq/MetaI.pm $(INST_LIB)/Bio/Graphics/Glyph/dot.pm $(INST_LIB)/Bio/Taxonomy.pm $(INST_LIB)/Bio/Phenotype/MeSH/Term.pm $(INST_LIB)/Bio/Align/DNAStatistics.pm
3389
$(RM_F) $(INST_LIB)/Bio/OntologyIO/Handlers/BaseSAXHandler.pm $(INST_LIB)/Bio/FeatureHolderI.pm $(INST_LIB)/Bio/TreeIO/TreeEventBuilder.pm $(INST_LIB)/Bio/SeqFeature/Gene/Exon.pm
3390
$(RM_F) $(INST_LIB)/Bio/Search/Hit/PsiBlastHit.pm $(INST_LIB)/Bio/Index/GenBank.pm $(INST_LIB)/Bio/DB/Fasta.pm $(INST_LIB)/Bio/Restriction/EnzymeI.pm $(INST_LIB)/Bio/PopGen/IO/csv.pm
3391
$(RM_F) $(INST_LIB)/Bio/Search/HSP/PsiBlastHSP.pm $(INST_LIB)/Bio/Root/Err.pm $(INST_LIB)/Bio/Index/Fasta.pm $(INST_LIB)/Bio/Tools/Run/RemoteBlast.pm $(INST_LIB)/Bio/SearchIO/blasttable.pm
3392
$(RM_F) $(INST_LIB)/Bio/Search/HSP/HSPI.pm $(INST_LIB)/Bio/Graphics/Glyph/ellipse.pm $(INST_LIB)/Bio/PopGen/PopStats.pm $(INST_LIB)/Bio/Seq/RichSeqI.pm $(INST_LIB)/Bio/DB/GFF/Adaptor/ace.pm
3393
$(RM_F) $(INST_LIB)/Bio/Tools/Run/README $(INST_LIB)/Bio/Tools/Genewise.pm $(INST_LIB)/Bio/SearchIO/psl.pm $(INST_LIB)/Bio/Taxonomy/Node.pm $(INST_LIB)/Bio/OntologyIO/goflat.pm
3394
$(RM_F) $(INST_LIB)/Bio/Graphics/Panel.pm $(INST_LIB)/Bio/Factory/SequenceStreamI.pm $(INST_LIB)/Bio/TreeIO/nhx.pm $(INST_LIB)/Bio/SeqIO/scf.pm $(INST_LIB)/Bio/DB/Flat/BDB/swiss.pm
3395
$(RM_F) $(INST_LIB)/Bio/Tools/Hmmpfam.pm $(INST_LIB)/Bio/Root/HTTPget.pm $(INST_LIB)/Bio/SearchIO/exonerate.pm $(INST_LIB)/Bio/Biblio/IO/medlinexml.pm $(INST_LIB)/Bio/Seq/SeqFastaSpeedFactory.pm
3396
$(RM_F) $(INST_LIB)/Bio/Symbol/Alphabet.pm $(INST_LIB)/Bio/Tools/Blast/HSP.pm $(INST_LIB)/Bio/SearchIO/Writer/HitTableWriter.pm $(INST_LIB)/Bio/Biblio/MedlineBookArticle.pm
3397
$(RM_F) $(INST_LIB)/Bio/Biblio/IO/pubmed2ref.pm $(INST_LIB)/Bio/Tools/Analysis/Protein/NetPhos.pm $(INST_LIB)/Bio/Search/Hit/GenericHit.pm $(INST_LIB)/Bio/Phenotype/PhenotypeI.pm
3398
$(RM_F) $(INST_LIB)/Bio/SeqIO/asciitree.pm $(INST_LIB)/Bio/Graphics/Glyph/group.pm $(INST_LIB)/Bio/Location/Fuzzy.pm $(INST_LIB)/Bio/DB/Biblio/biofetch.pm $(INST_LIB)/Bio/Root/Exception.pm
3399
$(RM_F) $(INST_LIB)/Bio/Tools/Analysis/Protein/HNN.pm $(INST_LIB)/Bio/Tools/pSW.pm $(INST_LIB)/Bio/SeqIO/game/gameSubs.pm $(INST_LIB)/Bio/Seq/SeqFactory.pm $(INST_LIB)/Bio/SearchIO/hmmer.pm
3400
$(RM_F) $(INST_LIB)/Bio/Seq/Meta/Array.pm $(INST_LIB)/Bio/OntologyIO/dagflat.pm $(INST_LIB)/Bio/Location/Simple.pm $(INST_LIB)/Bio/Graphics/Glyph/triangle.pm $(INST_LIB)/Bio/SeqFeature/Gene/TranscriptI.pm
3401
$(RM_F) $(INST_LIB)/Bio/Tools/Gel.pm $(INST_LIB)/Bio/Matrix/Scoring.pm $(INST_LIB)/Bio/Search/HSP/FastaHSP.pm $(INST_LIB)/Bio/DB/InMemoryCache.pm $(INST_LIB)/Bio/SeqIO/fasta.pm $(INST_LIB)/Bio/IdentifiableI.pm
3402
$(RM_F) $(INST_LIB)/Bio/Symbol/README.Symbol $(INST_LIB)/Bio/AlignIO/prodom.pm $(INST_LIB)/Bio/Location/AvWithinCoordPolicy.pm $(INST_LIB)/Bio/SeqIO/qual.pm $(INST_LIB)/Bio/Phenotype/OMIM/MiniMIMentry.pm
3403
$(RM_F) $(INST_LIB)/Bio/Root/IOManager.pm $(INST_LIB)/Bio/SearchIO/Writer/TextResultWriter.pm $(INST_LIB)/Bio/Root/RootI.pm $(INST_LIB)/Bio/Coordinate/Result/Match.pm $(INST_LIB)/Bio/Factory/ObjectFactory.pm
3404
$(RM_F) $(INST_LIB)/Bio/SeqIO/pir.pm $(INST_LIB)/Bio/SeqIO/ctf.pm $(INST_LIB)/Bio/Search/Hit/BlastHit.pm $(INST_LIB)/Bio/Restriction/IO/itype2.pm $(INST_LIB)/Bio/Ontology/RelationshipType.pm
3405
$(RM_F) $(INST_LIB)/Bio/DB/GFF/Aggregator/transcript.pm $(INST_LIB)/Bio/PopGen/PopulationI.pm $(INST_LIB)/Bio/Tools/Prediction/Exon.pm $(INST_LIB)/Bio/Tools/Analysis/Protein/Scansite.pm
3406
$(RM_F) $(INST_LIB)/Bio/AlignIO/mase.pm $(INST_LIB)/Bio/AlignIO/msf.pm $(INST_LIB)/Bio/SeqIO/embl.pm $(INST_LIB)/Bio/Search/Result/WABAResult.pm $(INST_LIB)/Bio/Matrix/PSM/SiteMatrix.pm
3407
$(RM_F) $(INST_LIB)/Bio/Tools/Glimmer.pm $(INST_LIB)/Bio/SeqFeature/Gene/GeneStructureI.pm $(INST_LIB)/Bio/Map/CytoMarker.pm $(INST_LIB)/Bio/DB/GFF/Homol.pm $(INST_LIB)/Bio/Root/Global.pm
3408
$(RM_F) $(INST_LIB)/Bio/SeqFeature/Gene/GeneStructure.pm $(INST_LIB)/Bio/Biblio/Service.pm $(INST_LIB)/Bio/WebAgent.pm $(INST_LIB)/Bio/DB/GFF/Aggregator/clone.pm $(INST_LIB)/Bio/AnalysisResultI.pm
3409
$(RM_F) $(INST_LIB)/Bio/Graphics/Glyph/redgreen_box.pm $(INST_LIB)/Bio/Seq/SeqBuilder.pm $(INST_LIB)/Bio/Biblio/Article.pm $(INST_LIB)/Bio/Matrix/PSM/SiteMatrixI.pm $(INST_LIB)/Bio/Biblio/Ref.pm
3410
$(RM_F) $(INST_LIB)/Bio/Structure/Entry.pm $(INST_LIB)/Bio/Map/PositionI.pm $(INST_LIB)/Bio/Graphics/Glyph/pinsertion.pm $(INST_LIB)/Bio/Coordinate/Collection.pm $(INST_LIB)/Bio/Graphics/Glyph/ex.pm
3411
$(RM_F) $(INST_LIB)/Bio/DB/GFF/Aggregator/ucsc_unigene.pm $(INST_LIB)/Bio/DB/GFF/Adaptor/dbi.pm $(INST_LIB)/Bio/Graphics/RendererI.pm $(INST_LIB)/Bio/DB/Taxonomy/entrez.pm $(INST_LIB)/Bio/Tree/Tree.pm
3412
$(RM_F) $(INST_LIB)/Bio/Variation/AAReverseMutate.pm $(INST_LIB)/Bio/LiveSeq/IO/Loader.pm $(INST_LIB)/Bio/Tools/SiRNA.pm $(INST_LIB)/Bio/Seq.pm $(INST_LIB)/Bio/Cluster/ClusterFactory.pm
3413
$(RM_F) $(INST_LIB)/Bio/Graphics/Glyph/box.pm $(INST_LIB)/Bio/Align/PairwiseStatistics.pm $(INST_LIB)/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm $(INST_LIB)/Bio/DB/GFF/Aggregator/ucsc_softberry.pm
3414
$(RM_F) $(INST_LIB)/Bio/SeqIO/game/featHandler.pm $(INST_LIB)/Bio/Expression/FeatureGroup.pm $(INST_LIB)/Bio/Symbol/SymbolI.pm $(INST_LIB)/Bio/IdCollectionI.pm $(INST_LIB)/Bio/Restriction/Enzyme/MultiSite.pm
3415
$(RM_F) $(INST_LIB)/Bio/AlignIO/clustalw.pm $(INST_LIB)/Bio/Phenotype/Phenotype.pm $(INST_LIB)/Bio/Tools/Genemark.pm $(INST_LIB)/Bio/LiveSeq/IO/README $(INST_LIB)/Bio/DB/GFF/Adaptor/memory.pm
3416
$(RM_F) $(INST_LIB)/Bio/Biblio/Thesis.pm $(INST_LIB)/Bio/Seq/BaseSeqProcessor.pm $(INST_LIB)/Bio/Location/NarrowestCoordPolicy.pm $(INST_LIB)/Bio/DB/NCBIHelper.pm
3417
$(RM_F) $(INST_LIB)/Bio/Expression/FeatureSet/FeatureSetMas50.pm $(INST_LIB)/Bio/SeqIO/alf.pm $(INST_LIB)/Bio/Tools/Primer/AssessorI.pm $(INST_LIB)/Bio/SeqFeature/Generic.pm
3418
$(RM_F) $(INST_LIB)/Bio/Graphics/Glyph/translation.pm $(INST_LIB)/Bio/Tools/OddCodes.pm $(INST_LIB)/Bio/Tools/Analysis/Protein/GOR4.pm $(INST_LIB)/Bio/ClusterIO.pm $(INST_LIB)/Bio/Coordinate/GeneMapper.pm
3419
$(RM_F) $(INST_LIB)/Bio/DB/Failover.pm $(INST_LIB)/Bio/AnnotatableI.pm $(INST_LIB)/Bio/SeqIO/pln.pm $(INST_LIB)/Bio/Tools/Phylo/PAML/ModelResult.pm $(INST_LIB)/Bio/Das/SegmentI.pm
3420
$(RM_F) $(INST_LIB)/Bio/Graphics/Glyph/rndrect.pm $(INST_LIB)/Bio/SearchIO/fasta.pm $(INST_LIB)/Bio/Restriction/Enzyme/MultiCut.pm $(INST_LIB)/Bio/Graphics/Glyph/track.pm $(INST_LIB)/Bio/Biblio/Journal.pm
3421
$(RM_F) $(INST_LIB)/Bio/Phenotype/OMIM/OMIMparser.pm $(INST_LIB)/Bio/Matrix/IO/scoring.pm $(INST_LIB)/Bio/ClusterIO/unigene.pm $(INST_LIB)/Bio/Tools/Alignment/Consed.pm $(INST_LIB)/Bio/AnnotationCollectionI.pm
3422
$(RM_F) $(INST_LIB)/Bio/DB/GFF/Aggregator/ucsc_genscan.pm $(INST_LIB)/Bio/Tools/BPpsilite.pm $(INST_LIB)/Bio/Tools/Primer/Feature.pm $(INST_LIB)/Bio/TreeIO/svggraph.pm
3423
$(RM_F) $(INST_LIB)/Bio/LiveSeq/Prim_Transcript.pm $(INST_LIB)/Bio/Seq/EncodedSeq.pm $(INST_LIB)/Bio/Matrix/PSM/Psm.pm $(INST_LIB)/Bio/Annotation/Reference.pm
3424
$(RM_F) $(INST_LIB)/Bio/SearchIO/IteratedSearchResultEventBuilder.pm $(INST_LIB)/Bio/Graphics/Glyph/generic.pm $(INST_LIB)/Bio/Matrix/IO/phylip.pm $(INST_LIB)/Bio/SimpleAnalysisI.pm
3425
$(RM_F) $(INST_LIB)/Bio/DB/Flat/BDB/fasta.pm $(INST_LIB)/Bio/Assembly/IO.pm $(INST_LIB)/Bio/DB/SwissProt.pm $(INST_LIB)/Bio/Ontology/PathI.pm $(INST_LIB)/Bio/DB/GFF/Adaptor/biofetch.pm
3426
$(RM_F) $(INST_LIB)/Bio/Tools/SeqWords.pm $(INST_LIB)/Bio/Assembly/Contig.pm $(INST_LIB)/Bio/Coordinate/Graph.pm $(INST_LIB)/Bio/Seq/QualI.pm $(INST_LIB)/Bio/Graphics/Glyph/line.pm
3427
$(RM_F) $(INST_LIB)/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm $(INST_LIB)/Bio/DB/GFF/Aggregator/ucsc_refgene.pm $(INST_LIB)/Bio/Graphics/Glyph/arrow.pm $(INST_LIB)/Bio/Coordinate/Result.pm
3428
$(RM_F) $(INST_LIB)/Bio/PopGen/IO.pm $(INST_LIB)/Bio/Phenotype/Correlate.pm $(INST_LIB)/Bio/Root/Root.pm $(INST_LIB)/Bio/Matrix/PSM/InstanceSiteI.pm $(INST_LIB)/Bio/Factory/DriverFactory.pm
3429
$(RM_F) $(INST_LIB)/Bio/Tools/RestrictionEnzyme.pm $(INST_LIB)/Bio/SeqI.pm $(INST_LIB)/Bio/Symbol/ProteinAlphabet.pm $(INST_LIB)/Bio/AlignIO/selex.pm $(INST_LIB)/Bio/Graphics/Glyph/primers.pm
3430
$(RM_F) $(INST_LIB)/Bio/Assembly/Scaffold.pm $(INST_LIB)/Bio/Annotation/StructuredValue.pm $(INST_LIB)/Bio/DB/GenPept.pm $(INST_LIB)/Bio/SeqFeature/Gene/UTR.pm $(INST_LIB)/Bio/TreeIO.pm
3431
$(RM_F) $(INST_LIB)/Bio/SearchIO/EventHandlerI.pm $(INST_LIB)/Bio/Ontology/TermI.pm $(INST_LIB)/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm $(INST_LIB)/Bio/Tree/Statistics.pm $(INST_LIB)/Bio/DB/DBFetch.pm
3432
$(RM_F) $(INST_LIB)/Bio/TreeIO/tabtree.pm $(INST_LIB)/Bio/PopGen/Population.pm
3433
3434
3435
# --- MakeMaker metafile section:
3436
metafile :
3437
$(NOECHO) $(ECHO) '# http://module-build.sourceforge.net/META-spec.html' > META.yml
3438
$(NOECHO) $(ECHO) '#XXXXXXX This is a prototype!!! It will change in the future!!! XXXXX#' >> META.yml
3439
$(NOECHO) $(ECHO) 'name: bioperl' >> META.yml
3440
$(NOECHO) $(ECHO) 'version: 1.4' >> META.yml
3441
$(NOECHO) $(ECHO) 'version_from: Bio/Root/Version.pm' >> META.yml
3442
$(NOECHO) $(ECHO) 'installdirs: site' >> META.yml
3443
$(NOECHO) $(ECHO) 'requires:' >> META.yml
3444
$(NOECHO) $(ECHO) ' DB_File: 0' >> META.yml
3445
$(NOECHO) $(ECHO) ' File::Spec: 0' >> META.yml
3446
$(NOECHO) $(ECHO) ' File::Temp: 0' >> META.yml
3447
$(NOECHO) $(ECHO) ' HTML::Entities: 0' >> META.yml
3448
$(NOECHO) $(ECHO) ' IO::Scalar: 0' >> META.yml
3449
$(NOECHO) $(ECHO) ' IO::String: 0' >> META.yml
3450
$(NOECHO) $(ECHO) '' >> META.yml
3451
$(NOECHO) $(ECHO) 'distribution_type: module' >> META.yml
3452
$(NOECHO) $(ECHO) 'generated_by: ExtUtils::MakeMaker version 6.17' >> META.yml
3453
3454
3455
# --- MakeMaker metafile_addtomanifest section:
3456
metafile_addtomanifest:
3457
$(NOECHO) $(PERLRUN) -MExtUtils::Manifest=maniadd -e 'eval { maniadd({q{META.yml} => q{Module meta-data (added by MakeMaker)}}) } ' \
3458
-e ' or print "Could not add META.yml to MANIFEST: $${'\''@'\''}\n"'
3459
3460
3461
# --- MakeMaker dist_basics section:
3462
distclean :: realclean distcheck
3463
$(NOECHO) $(NOOP)
3464
3465
distcheck :
3466
$(PERLRUN) "-MExtUtils::Manifest=fullcheck" -e fullcheck
3467
3468
skipcheck :
3469
$(PERLRUN) "-MExtUtils::Manifest=skipcheck" -e skipcheck
3470
3471
manifest :
3472
$(PERLRUN) "-MExtUtils::Manifest=mkmanifest" -e mkmanifest
3473
3474
veryclean : realclean
3475
$(RM_F) *~ *.orig */*~ */*.orig
3476
3477
3478
3479
# --- MakeMaker dist_core section:
3480
3481
dist : $(DIST_DEFAULT) $(FIRST_MAKEFILE)
3482
$(NOECHO) $(PERLRUN) -l -e 'print '\''Warning: Makefile possibly out of date with $(VERSION_FROM)'\''' \
3483
-e ' if -e '\''$(VERSION_FROM)'\'' and -M '\''$(VERSION_FROM)'\'' < -M '\''$(FIRST_MAKEFILE)'\'';'
3484
3485
tardist : $(DISTVNAME).tar$(SUFFIX)
3486
$(NOECHO) $(NOOP)
3487
3488
uutardist : $(DISTVNAME).tar$(SUFFIX)
3489
uuencode $(DISTVNAME).tar$(SUFFIX) $(DISTVNAME).tar$(SUFFIX) > $(DISTVNAME).tar$(SUFFIX)_uu
3490
3491
$(DISTVNAME).tar$(SUFFIX) : distdir
3492
$(PREOP)
3493
$(TO_UNIX)
3494
$(TAR) $(TARFLAGS) $(DISTVNAME).tar $(DISTVNAME)
3495
$(RM_RF) $(DISTVNAME)
3496
$(COMPRESS) $(DISTVNAME).tar
3497
$(POSTOP)
3498
3499
zipdist : $(DISTVNAME).zip
3500
$(NOECHO) $(NOOP)
3501
3502
$(DISTVNAME).zip : distdir
3503
$(PREOP)
3504
$(ZIP) $(ZIPFLAGS) $(DISTVNAME).zip $(DISTVNAME)
3505
$(RM_RF) $(DISTVNAME)
3506
$(POSTOP)
3507
3508
shdist : distdir
3509
$(PREOP)
3510
$(SHAR) $(DISTVNAME) > $(DISTVNAME).shar
3511
$(RM_RF) $(DISTVNAME)
3512
$(POSTOP)
3513
3514
3515
# --- MakeMaker distdir section:
3516
distdir : metafile metafile_addtomanifest
3517
$(RM_RF) $(DISTVNAME)
3518
$(PERLRUN) "-MExtUtils::Manifest=manicopy,maniread" \
3519
-e "manicopy(maniread(),'$(DISTVNAME)', '$(DIST_CP)');"
3520
3521
3522
3523
# --- MakeMaker dist_test section:
3524
3525
disttest : distdir
3526
cd $(DISTVNAME) && $(ABSPERLRUN) Makefile.PL
3527
cd $(DISTVNAME) && $(MAKE) $(PASTHRU)
3528
cd $(DISTVNAME) && $(MAKE) test $(PASTHRU)
3529
3530
3531
# --- MakeMaker dist_ci section:
3532
3533
ci :
3534
$(PERLRUN) "-MExtUtils::Manifest=maniread" \
3535
-e "@all = keys %{ maniread() };" \
3536
-e "print(qq{Executing $(CI) @all\n}); system(qq{$(CI) @all});" \
3537
-e "print(qq{Executing $(RCS_LABEL) ...\n}); system(qq{$(RCS_LABEL) @all});"
3538
3539
3540
# --- MakeMaker install section:
3541
3542
install :: all pure_install doc_install
3543
3544
install_perl :: all pure_perl_install doc_perl_install
3545
3546
install_site :: all pure_site_install doc_site_install
3547
3548
install_vendor :: all pure_vendor_install doc_vendor_install
3549
3550
pure_install :: pure_$(INSTALLDIRS)_install
3551
3552
doc_install :: doc_$(INSTALLDIRS)_install
3553
3554
pure__install : pure_site_install
3555
$(NOECHO) $(ECHO) INSTALLDIRS not defined, defaulting to INSTALLDIRS=site
3556
3557
doc__install : doc_site_install
3558
$(NOECHO) $(ECHO) INSTALLDIRS not defined, defaulting to INSTALLDIRS=site
3559
3560
pure_perl_install ::
3561
$(NOECHO) $(MOD_INSTALL) \
3562
read $(PERL_ARCHLIB)/auto/$(FULLEXT)/.packlist \
3563
write $(DESTINSTALLARCHLIB)/auto/$(FULLEXT)/.packlist \
3564
$(INST_LIB) $(DESTINSTALLPRIVLIB) \
3565
$(INST_ARCHLIB) $(DESTINSTALLARCHLIB) \
3566
$(INST_BIN) $(DESTINSTALLBIN) \
3567
$(INST_SCRIPT) $(DESTINSTALLSCRIPT) \
3568
$(INST_MAN1DIR) $(DESTINSTALLMAN1DIR) \
3569
$(INST_MAN3DIR) $(DESTINSTALLMAN3DIR)
3570
$(NOECHO) $(WARN_IF_OLD_PACKLIST) \
3571
$(SITEARCHEXP)/auto/$(FULLEXT)
3572
3573
3574
pure_site_install ::
3575
$(NOECHO) $(MOD_INSTALL) \
3576
read $(SITEARCHEXP)/auto/$(FULLEXT)/.packlist \
3577
write $(DESTINSTALLSITEARCH)/auto/$(FULLEXT)/.packlist \
3578
$(INST_LIB) $(DESTINSTALLSITELIB) \
3579
$(INST_ARCHLIB) $(DESTINSTALLSITEARCH) \
3580
$(INST_BIN) $(DESTINSTALLSITEBIN) \
3581
$(INST_SCRIPT) $(DESTINSTALLSCRIPT) \
3582
$(INST_MAN1DIR) $(DESTINSTALLSITEMAN1DIR) \
3583
$(INST_MAN3DIR) $(DESTINSTALLSITEMAN3DIR)
3584
$(NOECHO) $(WARN_IF_OLD_PACKLIST) \
3585
$(PERL_ARCHLIB)/auto/$(FULLEXT)
3586
3587
pure_vendor_install ::
3588
$(NOECHO) $(MOD_INSTALL) \
3589
read $(VENDORARCHEXP)/auto/$(FULLEXT)/.packlist \
3590
write $(DESTINSTALLVENDORARCH)/auto/$(FULLEXT)/.packlist \
3591
$(INST_LIB) $(DESTINSTALLVENDORLIB) \
3592
$(INST_ARCHLIB) $(DESTINSTALLVENDORARCH) \
3593
$(INST_BIN) $(DESTINSTALLVENDORBIN) \
3594
$(INST_SCRIPT) $(DESTINSTALLSCRIPT) \
3595
$(INST_MAN1DIR) $(DESTINSTALLVENDORMAN1DIR) \
3596
$(INST_MAN3DIR) $(DESTINSTALLVENDORMAN3DIR)
3597
3598
doc_perl_install ::
3599
$(NOECHO) $(ECHO) Appending installation info to $(DESTINSTALLARCHLIB)/perllocal.pod
3600
-$(NOECHO) $(MKPATH) $(DESTINSTALLARCHLIB)
3601
-$(NOECHO) $(DOC_INSTALL) \
3602
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3603
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3604
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3605
VERSION "$(VERSION)" \
3606
EXE_FILES "$(EXE_FILES)" \
3607
>> $(DESTINSTALLARCHLIB)/perllocal.pod
3608
3609
doc_site_install ::
3610
$(NOECHO) $(ECHO) Appending installation info to $(DESTINSTALLARCHLIB)/perllocal.pod
3611
-$(NOECHO) $(MKPATH) $(DESTINSTALLARCHLIB)
3612
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3613
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3614
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3616
VERSION "$(VERSION)" \
3617
EXE_FILES "$(EXE_FILES)" \
3618
>> $(DESTINSTALLARCHLIB)/perllocal.pod
3619
3620
doc_vendor_install ::
3621
$(NOECHO) $(ECHO) Appending installation info to $(DESTINSTALLARCHLIB)/perllocal.pod
3622
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3623
-$(NOECHO) $(DOC_INSTALL) \
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3625
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3626
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3627
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3628
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3629
>> $(DESTINSTALLARCHLIB)/perllocal.pod
3630
3631
3632
uninstall :: uninstall_from_$(INSTALLDIRS)dirs
3633
3634
uninstall_from_perldirs ::
3635
$(NOECHO) $(UNINSTALL) $(PERL_ARCHLIB)/auto/$(FULLEXT)/.packlist
3636
3637
uninstall_from_sitedirs ::
3638
$(NOECHO) $(UNINSTALL) $(SITEARCHEXP)/auto/$(FULLEXT)/.packlist
3639
3640
uninstall_from_vendordirs ::
3641
$(NOECHO) $(UNINSTALL) $(VENDORARCHEXP)/auto/$(FULLEXT)/.packlist
3642
3643
3644
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3645
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3646
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3647
$(NOECHO) $(NOOP)
3648
3649
3650
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3651
3652
3653
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3655
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3656
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3657
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3668
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3671
3672
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3673
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3675
3676
$(MAP_TARGET) :: static $(MAKE_APERL_FILE)
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$(MAKE) -f $(MAKE_APERL_FILE) $@
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$(MAKE_APERL_FILE) : $(FIRST_MAKEFILE)
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$(NOECHO) $(ECHO) Writing \"$(MAKE_APERL_FILE)\" for this $(MAP_TARGET)
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$(NOECHO) $(PERLRUNINST) \
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Makefile.PL DIR= \
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MAKEFILE=$(MAKE_APERL_FILE) LINKTYPE=static \
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3685
3686
3687
# --- MakeMaker test section:
3688
3689
TEST_VERBOSE=0
3690
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3691
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3692
TEST_FILES = t/*.t
3693
TESTDB_SW = -d
3694
3695
testdb :: testdb_$(LINKTYPE)
3696
3697
test :: $(TEST_TYPE)
3698
3699
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3700
PERL_DL_NONLAZY=1 $(FULLPERLRUN) "-MExtUtils::Command::MM" "-e" "test_harness($(TEST_VERBOSE), '$(INST_LIB)', '$(INST_ARCHLIB)')" $(TEST_FILES)
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testdb_dynamic :: pure_all
3703
PERL_DL_NONLAZY=1 $(FULLPERLRUN) $(TESTDB_SW) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE)
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3705
test_ : test_dynamic
3706
3707
test_static :: test_dynamic
3708
testdb_static :: testdb_dynamic
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3711
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3712
# Creates a PPD (Perl Package Description) for a binary distribution.
3713
ppd:
3714
$(NOECHO) $(ECHO) '<SOFTPKG NAME="$(DISTNAME)" VERSION="1,4,0,0">' > $(DISTNAME).ppd
3715
$(NOECHO) $(ECHO) ' <TITLE>$(DISTNAME)</TITLE>' >> $(DISTNAME).ppd
3716
$(NOECHO) $(ECHO) ' <ABSTRACT>Bioinformatics Toolkit</ABSTRACT>' >> $(DISTNAME).ppd
3717
$(NOECHO) $(ECHO) ' <AUTHOR>Bioperl Team (bioperl-l@bioperl.org)</AUTHOR>' >> $(DISTNAME).ppd
3718
$(NOECHO) $(ECHO) ' <IMPLEMENTATION>' >> $(DISTNAME).ppd
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$(NOECHO) $(ECHO) ' <DEPENDENCY NAME="DB_File" VERSION="0,0,0,0" />' >> $(DISTNAME).ppd
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$(NOECHO) $(ECHO) ' <DEPENDENCY NAME="File-Spec" VERSION="0,0,0,0" />' >> $(DISTNAME).ppd
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$(NOECHO) $(ECHO) ' <DEPENDENCY NAME="IO-Scalar" VERSION="0,0,0,0" />' >> $(DISTNAME).ppd
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$(NOECHO) $(ECHO) ' <DEPENDENCY NAME="IO-String" VERSION="0,0,0,0" />' >> $(DISTNAME).ppd
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$(NOECHO) $(ECHO) ' <OS NAME="$(OSNAME)" />' >> $(DISTNAME).ppd
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$(NOECHO) $(ECHO) ' <ARCHITECTURE NAME="i386-linux-thread-multi" />' >> $(DISTNAME).ppd
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$(NOECHO) $(ECHO) ' <CODEBASE HREF="" />' >> $(DISTNAME).ppd
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$(NOECHO) $(ECHO) ' </IMPLEMENTATION>' >> $(DISTNAME).ppd
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$(NOECHO) $(ECHO) '</SOFTPKG>' >> $(DISTNAME).ppd
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3732
# --- MakeMaker pm_to_blib section:
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3734
pm_to_blib: $(TO_INST_PM)
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$(NOECHO) $(PERLRUN) -MExtUtils::Install -e 'pm_to_blib({@ARGV}, '\''$(INST_LIB)/auto'\'', '\''$(PM_FILTER)'\'')'\
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Bio/WebAgent.pm $(INST_LIB)/Bio/WebAgent.pm \
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Bio/Factory/ObjectFactory.pm $(INST_LIB)/Bio/Factory/ObjectFactory.pm \
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Bio/SearchIO/megablast.pm $(INST_LIB)/Bio/SearchIO/megablast.pm \
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Bio/Factory/SeqAnalysisParserFactoryI.pm $(INST_LIB)/Bio/Factory/SeqAnalysisParserFactoryI.pm \
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Bio/Search/HSP/PSLHSP.pm $(INST_LIB)/Bio/Search/HSP/PSLHSP.pm \
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Bio/Cluster/UniGeneI.pm $(INST_LIB)/Bio/Cluster/UniGeneI.pm \
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Bio/Tools/GuessSeqFormat.pm $(INST_LIB)/Bio/Tools/GuessSeqFormat.pm \
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Bio/Tools/Run/README $(INST_LIB)/Bio/Tools/Run/README \
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Bio/DB/SwissProt.pm $(INST_LIB)/Bio/DB/SwissProt.pm \
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Bio/DB/GFF/Aggregator/ucsc_sanger22.pm $(INST_LIB)/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm \
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Bio/Root/RootI.pm $(INST_LIB)/Bio/Root/RootI.pm \
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Bio/LocationI.pm $(INST_LIB)/Bio/LocationI.pm \
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Bio/TreeIO/TreeEventBuilder.pm $(INST_LIB)/Bio/TreeIO/TreeEventBuilder.pm \
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Bio/Matrix/PSM/PsmI.pm $(INST_LIB)/Bio/Matrix/PSM/PsmI.pm \
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Bio/Taxonomy.pm $(INST_LIB)/Bio/Taxonomy.pm \
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Bio/Location/Fuzzy.pm $(INST_LIB)/Bio/Location/Fuzzy.pm \
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Bio/SeqIO.pm $(INST_LIB)/Bio/SeqIO.pm \
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Bio/AnalysisI.pm $(INST_LIB)/Bio/AnalysisI.pm \
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Bio/LiveSeq/AARange.pm $(INST_LIB)/Bio/LiveSeq/AARange.pm \
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Bio/DB/Biblio/biofetch.pm $(INST_LIB)/Bio/DB/Biblio/biofetch.pm \
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Bio/Index/Swissprot.pm $(INST_LIB)/Bio/Index/Swissprot.pm \
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Bio/Annotation/OntologyTerm.pm $(INST_LIB)/Bio/Annotation/OntologyTerm.pm \
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Bio/Map/SimpleMap.pm $(INST_LIB)/Bio/Map/SimpleMap.pm \
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Bio/Coordinate/Result/Gap.pm $(INST_LIB)/Bio/Coordinate/Result/Gap.pm \
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Bio/SearchIO/blasttable.pm $(INST_LIB)/Bio/SearchIO/blasttable.pm \
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Bio/Seq/BaseSeqProcessor.pm $(INST_LIB)/Bio/Seq/BaseSeqProcessor.pm \
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Bio/Seq/TraceI.pm $(INST_LIB)/Bio/Seq/TraceI.pm \
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Bio/Phenotype/Phenotype.pm $(INST_LIB)/Bio/Phenotype/Phenotype.pm \
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Bio/Seq/PrimaryQual.pm $(INST_LIB)/Bio/Seq/PrimaryQual.pm \
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Bio/Variation/Allele.pm $(INST_LIB)/Bio/Variation/Allele.pm \
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Bio/DB/Failover.pm $(INST_LIB)/Bio/DB/Failover.pm \
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Bio/LiveSeq/IO/Loader.pm $(INST_LIB)/Bio/LiveSeq/IO/Loader.pm \
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Bio/DB/UpdateableSeqI.pm $(INST_LIB)/Bio/DB/UpdateableSeqI.pm \
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Bio/DB/RefSeq.pm $(INST_LIB)/Bio/DB/RefSeq.pm \
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Bio/Coordinate/Result/Match.pm $(INST_LIB)/Bio/Coordinate/Result/Match.pm \
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Bio/Graphics/Glyph/group.pm $(INST_LIB)/Bio/Graphics/Glyph/group.pm \
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Bio/SimpleAnalysisI.pm $(INST_LIB)/Bio/SimpleAnalysisI.pm \
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Bio/Tools/Gel.pm $(INST_LIB)/Bio/Tools/Gel.pm \
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Bio/DB/NCBIHelper.pm $(INST_LIB)/Bio/DB/NCBIHelper.pm \
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Bio/Biblio/BiblioBase.pm $(INST_LIB)/Bio/Biblio/BiblioBase.pm \
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Bio/Biblio/IO.pm $(INST_LIB)/Bio/Biblio/IO.pm \
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Bio/Event/EventHandlerI.pm $(INST_LIB)/Bio/Event/EventHandlerI.pm \
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Bio/Graphics/Glyph/minmax.pm $(INST_LIB)/Bio/Graphics/Glyph/minmax.pm \
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Bio/Biblio.pm $(INST_LIB)/Bio/Biblio.pm \
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Bio/Phenotype/OMIM/OMIMparser.pm $(INST_LIB)/Bio/Phenotype/OMIM/OMIMparser.pm \
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Bio/SeqIO/ctf.pm $(INST_LIB)/Bio/SeqIO/ctf.pm \
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Bio/Tools/SeqPattern.pm $(INST_LIB)/Bio/Tools/SeqPattern.pm \
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Bio/LiveSeq/DNA.pm $(INST_LIB)/Bio/LiveSeq/DNA.pm \
3859
Bio/Index/AbstractSeq.pm $(INST_LIB)/Bio/Index/AbstractSeq.pm \
3860
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Bio/Tree/NodeI.pm $(INST_LIB)/Bio/Tree/NodeI.pm \
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Bio/Tools/Prints.pm $(INST_LIB)/Bio/Tools/Prints.pm \
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Bio/Map/OrderedPositionWithDistance.pm $(INST_LIB)/Bio/Map/OrderedPositionWithDistance.pm \
4431
Bio/SeqIO/game.pm $(INST_LIB)/Bio/SeqIO/game.pm \
4432
Bio/Biblio/IO/pubmed2ref.pm $(INST_LIB)/Bio/Biblio/IO/pubmed2ref.pm \
4433
Bio/Index/Abstract.pm $(INST_LIB)/Bio/Index/Abstract.pm \
4434
Bio/Tools/HMMER/Domain.pm $(INST_LIB)/Bio/Tools/HMMER/Domain.pm \
4435
Bio/Search/Iteration/IterationI.pm $(INST_LIB)/Bio/Search/Iteration/IterationI.pm \
4436
Bio/SearchIO/blastxml.pm $(INST_LIB)/Bio/SearchIO/blastxml.pm \
4437
Bio/DB/GFF/Adaptor/dbi/oracle.pm $(INST_LIB)/Bio/DB/GFF/Adaptor/dbi/oracle.pm \
4438
Bio/Biblio/IO/medlinexml.pm $(INST_LIB)/Bio/Biblio/IO/medlinexml.pm \
4439
Bio/Coordinate/GeneMapper.pm $(INST_LIB)/Bio/Coordinate/GeneMapper.pm \
4440
Bio/SeqIO/ace.pm $(INST_LIB)/Bio/SeqIO/ace.pm \
4441
Bio/Location/FuzzyLocationI.pm $(INST_LIB)/Bio/Location/FuzzyLocationI.pm \
4442
Bio/Search/Hit/Fasta.pm $(INST_LIB)/Bio/Search/Hit/Fasta.pm \
4443
Bio/Root/Exception.pm $(INST_LIB)/Bio/Root/Exception.pm \
4444
Bio/Factory/TreeFactoryI.pm $(INST_LIB)/Bio/Factory/TreeFactoryI.pm \
4445
Bio/Assembly/IO/ace.pm $(INST_LIB)/Bio/Assembly/IO/ace.pm \
4446
Bio/DB/Biblio/soap.pm $(INST_LIB)/Bio/DB/Biblio/soap.pm \
4447
Bio/SeqIO/tab.pm $(INST_LIB)/Bio/SeqIO/tab.pm \
4448
Bio/Root/Object.pm $(INST_LIB)/Bio/Root/Object.pm
4449
$(NOECHO) $(TOUCH) $@
4450
4451
# --- MakeMaker selfdocument section:
4452
4453
4454
# --- MakeMaker postamble section:
4455
show_tests :
4456
@echo 'type make test_<subtest> to run'
4457
@echo 'AAChange \
4458
AAReverseMutate \
4459
AlignIO \
4460
AlignStats \
4461
Allele \
4462
Alphabet \
4463
Annotation \
4464
AnnotationAdaptor \
4465
Assembly \
4466
BPbl2seq \
4467
BPlite \
4468
BPpsilite \
4469
Biblio \
4470
BiblioReferences \
4471
Biblio_biofetch \
4472
BioDBGFF \
4473
BioFetch_DB \
4474
BioGraphics \
4475
BlastIndex \
4476
Chain \
4477
ClusterIO \
4478
Coalescent \
4479
CodonTable \
4480
CoordinateGraph \
4481
CoordinateMapper \
4482
Correlate \
4483
CytoMap \
4484
DB \
4485
DBCUTG \
4486
DBFasta \
4487
DNAMutation \
4488
Domcut \
4489
ECnumber \
4490
ELM \
4491
EMBL_DB \
4492
EMBOSS_Tools \
4493
ESEfinder \
4494
EncodedSeq \
4495
Exception \
4496
Exonerate \
4497
FootPrinter \
4498
GDB \
4499
GFF \
4500
GOR4 \
4501
GOterm \
4502
GeneCoordinateMapper \
4503
Geneid \
4504
Genewise \
4505
Genomewise \
4506
Genpred \
4507
GuessSeqFormat \
4508
HNN \
4509
IUPAC \
4510
Index \
4511
InstanceSite \
4512
InterProParser \
4513
LinkageMap \
4514
LiveSeq \
4515
LocatableSeq \
4516
Location \
4517
LocationFactory \
4518
LocusLink \
4519
Map \
4520
MapIO \
4521
Matrix \
4522
MeSH \
4523
Measure \
4524
MetaSeq \
4525
MicrosatelliteMarker \
4526
MiniMIMentry \
4527
MitoProt \
4528
Molphy \
4529
Mutation \
4530
Mutator \
4531
NetPhos \
4532
Node \
4533
OMIMentry \
4534
OMIMentryAllelicVariant \
4535
OMIMparser \
4536
OddCodes \
4537
Ontology \
4538
OntologyEngine \
4539
PAML \
4540
Perl \
4541
Phenotype \
4542
PhylipDist \
4543
Pictogram \
4544
PopGen \
4545
PopGenSims \
4546
PrimarySeq \
4547
Primer \
4548
Promoterwise \
4549
ProtDist \
4550
QRNA \
4551
RNAChange \
4552
RandDistFunctions \
4553
RandomTreeFactory \
4554
Range \
4555
RangeI \
4556
RefSeq \
4557
Registry \
4558
Relationship \
4559
RelationshipType \
4560
RemoteBlast \
4561
RepeatMasker \
4562
RestrictionAnalysis \
4563
RestrictionEnzyme \
4564
RestrictionIO \
4565
RootI \
4566
RootIO \
4567
RootStorable \
4568
SNP \
4569
Scansite \
4570
SearchDist \
4571
SearchIO \
4572
Seq \
4573
SeqAnalysisParser \
4574
SeqBuilder \
4575
SeqDiff \
4576
SeqFeatCollection \
4577
SeqFeature \
4578
SeqIO \
4579
SeqPattern \
4580
SeqStats \
4581
SeqUtils \
4582
SeqWords \
4583
SequenceFamily \
4584
Sigcleave \
4585
Sim4 \
4586
SimilarityPair \
4587
SimpleAlign \
4588
SiteMatrix \
4589
Sopma \
4590
Species \
4591
StandAloneBlast \
4592
StructIO \
4593
Structure \
4594
Swiss \
4595
Symbol \
4596
Taxonomy \
4597
Tempfile \
4598
Term \
4599
Tools \
4600
Tree \
4601
TreeIO \
4602
UCSCParsers \
4603
Unflattener \
4604
Unflattener2 \
4605
UniGene \
4606
Variation_IO \
4607
WABA \
4608
XEMBL_DB \
4609
cigarstring \
4610
consed \
4611
ePCR \
4612
est2genome \
4613
flat \
4614
game \
4615
hmmer \
4616
largefasta \
4617
largepseq \
4618
lucy \
4619
multiple_fasta \
4620
pICalculator \
4621
phd \
4622
primaryqual \
4623
primedseq \
4624
primer3 \
4625
psm \
4626
qual \
4627
scf \
4628
seqfeaturePrimer \
4629
sequencetrace \
4630
seqwithquality \
4631
simpleGOparser \
4632
sirna \
4633
splicedseq \
4634
trim \
4635
tutorial \
4636
'
4637
test_AAChange :: pure_all
4638
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/AAChange.t
4639
test_AAReverseMutate :: pure_all
4640
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/AAReverseMutate.t
4641
test_AlignIO :: pure_all
4642
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/AlignIO.t
4643
test_AlignStats :: pure_all
4644
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/AlignStats.t
4645
test_Allele :: pure_all
4646
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Allele.t
4647
test_Alphabet :: pure_all
4648
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Alphabet.t
4649
test_Annotation :: pure_all
4650
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Annotation.t
4651
test_AnnotationAdaptor :: pure_all
4652
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/AnnotationAdaptor.t
4653
test_Assembly :: pure_all
4654
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Assembly.t
4655
test_BPbl2seq :: pure_all
4656
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/BPbl2seq.t
4657
test_BPlite :: pure_all
4658
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/BPlite.t
4659
test_BPpsilite :: pure_all
4660
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/BPpsilite.t
4661
test_Biblio :: pure_all
4662
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Biblio.t
4663
test_BiblioReferences :: pure_all
4664
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/BiblioReferences.t
4665
test_Biblio_biofetch :: pure_all
4666
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Biblio_biofetch.t
4667
test_BioDBGFF :: pure_all
4668
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/BioDBGFF.t
4669
test_BioFetch_DB :: pure_all
4670
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/BioFetch_DB.t
4671
test_BioGraphics :: pure_all
4672
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/BioGraphics.t
4673
test_BlastIndex :: pure_all
4674
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/BlastIndex.t
4675
test_Chain :: pure_all
4676
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Chain.t
4677
test_ClusterIO :: pure_all
4678
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/ClusterIO.t
4679
test_Coalescent :: pure_all
4680
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Coalescent.t
4681
test_CodonTable :: pure_all
4682
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/CodonTable.t
4683
test_CoordinateGraph :: pure_all
4684
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/CoordinateGraph.t
4685
test_CoordinateMapper :: pure_all
4686
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/CoordinateMapper.t
4687
test_Correlate :: pure_all
4688
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Correlate.t
4689
test_CytoMap :: pure_all
4690
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/CytoMap.t
4691
test_DB :: pure_all
4692
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/DB.t
4693
test_DBCUTG :: pure_all
4694
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/DBCUTG.t
4695
test_DBFasta :: pure_all
4696
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/DBFasta.t
4697
test_DNAMutation :: pure_all
4698
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/DNAMutation.t
4699
test_Domcut :: pure_all
4700
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Domcut.t
4701
test_ECnumber :: pure_all
4702
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/ECnumber.t
4703
test_ELM :: pure_all
4704
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/ELM.t
4705
test_EMBL_DB :: pure_all
4706
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/EMBL_DB.t
4707
test_EMBOSS_Tools :: pure_all
4708
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/EMBOSS_Tools.t
4709
test_ESEfinder :: pure_all
4710
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/ESEfinder.t
4711
test_EncodedSeq :: pure_all
4712
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/EncodedSeq.t
4713
test_Exception :: pure_all
4714
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Exception.t
4715
test_Exonerate :: pure_all
4716
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Exonerate.t
4717
test_FootPrinter :: pure_all
4718
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/FootPrinter.t
4719
test_GDB :: pure_all
4720
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/GDB.t
4721
test_GFF :: pure_all
4722
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/GFF.t
4723
test_GOR4 :: pure_all
4724
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/GOR4.t
4725
test_GOterm :: pure_all
4726
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/GOterm.t
4727
test_GeneCoordinateMapper :: pure_all
4728
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/GeneCoordinateMapper.t
4729
test_Geneid :: pure_all
4730
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Geneid.t
4731
test_Genewise :: pure_all
4732
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Genewise.t
4733
test_Genomewise :: pure_all
4734
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Genomewise.t
4735
test_Genpred :: pure_all
4736
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Genpred.t
4737
test_GuessSeqFormat :: pure_all
4738
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/GuessSeqFormat.t
4739
test_HNN :: pure_all
4740
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/HNN.t
4741
test_IUPAC :: pure_all
4742
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/IUPAC.t
4743
test_Index :: pure_all
4744
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Index.t
4745
test_InstanceSite :: pure_all
4746
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/InstanceSite.t
4747
test_InterProParser :: pure_all
4748
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/InterProParser.t
4749
test_LinkageMap :: pure_all
4750
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/LinkageMap.t
4751
test_LiveSeq :: pure_all
4752
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/LiveSeq.t
4753
test_LocatableSeq :: pure_all
4754
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/LocatableSeq.t
4755
test_Location :: pure_all
4756
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Location.t
4757
test_LocationFactory :: pure_all
4758
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/LocationFactory.t
4759
test_LocusLink :: pure_all
4760
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/LocusLink.t
4761
test_Map :: pure_all
4762
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Map.t
4763
test_MapIO :: pure_all
4764
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/MapIO.t
4765
test_Matrix :: pure_all
4766
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Matrix.t
4767
test_MeSH :: pure_all
4768
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/MeSH.t
4769
test_Measure :: pure_all
4770
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Measure.t
4771
test_MetaSeq :: pure_all
4772
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/MetaSeq.t
4773
test_MicrosatelliteMarker :: pure_all
4774
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/MicrosatelliteMarker.t
4775
test_MiniMIMentry :: pure_all
4776
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/MiniMIMentry.t
4777
test_MitoProt :: pure_all
4778
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/MitoProt.t
4779
test_Molphy :: pure_all
4780
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Molphy.t
4781
test_Mutation :: pure_all
4782
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Mutation.t
4783
test_Mutator :: pure_all
4784
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Mutator.t
4785
test_NetPhos :: pure_all
4786
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/NetPhos.t
4787
test_Node :: pure_all
4788
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Node.t
4789
test_OMIMentry :: pure_all
4790
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/OMIMentry.t
4791
test_OMIMentryAllelicVariant :: pure_all
4792
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/OMIMentryAllelicVariant.t
4793
test_OMIMparser :: pure_all
4794
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/OMIMparser.t
4795
test_OddCodes :: pure_all
4796
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/OddCodes.t
4797
test_Ontology :: pure_all
4798
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Ontology.t
4799
test_OntologyEngine :: pure_all
4800
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/OntologyEngine.t
4801
test_PAML :: pure_all
4802
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/PAML.t
4803
test_Perl :: pure_all
4804
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Perl.t
4805
test_Phenotype :: pure_all
4806
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Phenotype.t
4807
test_PhylipDist :: pure_all
4808
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/PhylipDist.t
4809
test_Pictogram :: pure_all
4810
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Pictogram.t
4811
test_PopGen :: pure_all
4812
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/PopGen.t
4813
test_PopGenSims :: pure_all
4814
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/PopGenSims.t
4815
test_PrimarySeq :: pure_all
4816
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/PrimarySeq.t
4817
test_Primer :: pure_all
4818
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Primer.t
4819
test_Promoterwise :: pure_all
4820
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Promoterwise.t
4821
test_ProtDist :: pure_all
4822
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/ProtDist.t
4823
test_QRNA :: pure_all
4824
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/QRNA.t
4825
test_RNAChange :: pure_all
4826
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/RNAChange.t
4827
test_RandDistFunctions :: pure_all
4828
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/RandDistFunctions.t
4829
test_RandomTreeFactory :: pure_all
4830
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/RandomTreeFactory.t
4831
test_Range :: pure_all
4832
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Range.t
4833
test_RangeI :: pure_all
4834
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/RangeI.t
4835
test_RefSeq :: pure_all
4836
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/RefSeq.t
4837
test_Registry :: pure_all
4838
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Registry.t
4839
test_Relationship :: pure_all
4840
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Relationship.t
4841
test_RelationshipType :: pure_all
4842
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/RelationshipType.t
4843
test_RemoteBlast :: pure_all
4844
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/RemoteBlast.t
4845
test_RepeatMasker :: pure_all
4846
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/RepeatMasker.t
4847
test_RestrictionAnalysis :: pure_all
4848
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/RestrictionAnalysis.t
4849
test_RestrictionEnzyme :: pure_all
4850
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/RestrictionEnzyme.t
4851
test_RestrictionIO :: pure_all
4852
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/RestrictionIO.t
4853
test_RootI :: pure_all
4854
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/RootI.t
4855
test_RootIO :: pure_all
4856
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/RootIO.t
4857
test_RootStorable :: pure_all
4858
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/RootStorable.t
4859
test_SNP :: pure_all
4860
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/SNP.t
4861
test_Scansite :: pure_all
4862
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Scansite.t
4863
test_SearchDist :: pure_all
4864
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/SearchDist.t
4865
test_SearchIO :: pure_all
4866
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/SearchIO.t
4867
test_Seq :: pure_all
4868
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Seq.t
4869
test_SeqAnalysisParser :: pure_all
4870
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/SeqAnalysisParser.t
4871
test_SeqBuilder :: pure_all
4872
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/SeqBuilder.t
4873
test_SeqDiff :: pure_all
4874
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/SeqDiff.t
4875
test_SeqFeatCollection :: pure_all
4876
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/SeqFeatCollection.t
4877
test_SeqFeature :: pure_all
4878
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/SeqFeature.t
4879
test_SeqIO :: pure_all
4880
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/SeqIO.t
4881
test_SeqPattern :: pure_all
4882
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/SeqPattern.t
4883
test_SeqStats :: pure_all
4884
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/SeqStats.t
4885
test_SeqUtils :: pure_all
4886
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/SeqUtils.t
4887
test_SeqWords :: pure_all
4888
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/SeqWords.t
4889
test_SequenceFamily :: pure_all
4890
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/SequenceFamily.t
4891
test_Sigcleave :: pure_all
4892
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Sigcleave.t
4893
test_Sim4 :: pure_all
4894
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Sim4.t
4895
test_SimilarityPair :: pure_all
4896
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/SimilarityPair.t
4897
test_SimpleAlign :: pure_all
4898
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/SimpleAlign.t
4899
test_SiteMatrix :: pure_all
4900
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/SiteMatrix.t
4901
test_Sopma :: pure_all
4902
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Sopma.t
4903
test_Species :: pure_all
4904
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Species.t
4905
test_StandAloneBlast :: pure_all
4906
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/StandAloneBlast.t
4907
test_StructIO :: pure_all
4908
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/StructIO.t
4909
test_Structure :: pure_all
4910
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Structure.t
4911
test_Swiss :: pure_all
4912
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Swiss.t
4913
test_Symbol :: pure_all
4914
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Symbol.t
4915
test_Taxonomy :: pure_all
4916
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Taxonomy.t
4917
test_Tempfile :: pure_all
4918
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Tempfile.t
4919
test_Term :: pure_all
4920
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Term.t
4921
test_Tools :: pure_all
4922
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Tools.t
4923
test_Tree :: pure_all
4924
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Tree.t
4925
test_TreeIO :: pure_all
4926
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/TreeIO.t
4927
test_UCSCParsers :: pure_all
4928
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/UCSCParsers.t
4929
test_Unflattener :: pure_all
4930
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Unflattener.t
4931
test_Unflattener2 :: pure_all
4932
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Unflattener2.t
4933
test_UniGene :: pure_all
4934
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/UniGene.t
4935
test_Variation_IO :: pure_all
4936
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/Variation_IO.t
4937
test_WABA :: pure_all
4938
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/WABA.t
4939
test_XEMBL_DB :: pure_all
4940
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/XEMBL_DB.t
4941
test_cigarstring :: pure_all
4942
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/cigarstring.t
4943
test_consed :: pure_all
4944
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/consed.t
4945
test_ePCR :: pure_all
4946
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/ePCR.t
4947
test_est2genome :: pure_all
4948
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/est2genome.t
4949
test_flat :: pure_all
4950
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/flat.t
4951
test_game :: pure_all
4952
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/game.t
4953
test_hmmer :: pure_all
4954
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/hmmer.t
4955
test_largefasta :: pure_all
4956
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/largefasta.t
4957
test_largepseq :: pure_all
4958
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/largepseq.t
4959
test_lucy :: pure_all
4960
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/lucy.t
4961
test_multiple_fasta :: pure_all
4962
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/multiple_fasta.t
4963
test_pICalculator :: pure_all
4964
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/pICalculator.t
4965
test_phd :: pure_all
4966
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/phd.t
4967
test_primaryqual :: pure_all
4968
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/primaryqual.t
4969
test_primedseq :: pure_all
4970
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/primedseq.t
4971
test_primer3 :: pure_all
4972
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/primer3.t
4973
test_psm :: pure_all
4974
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/psm.t
4975
test_qual :: pure_all
4976
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/qual.t
4977
test_scf :: pure_all
4978
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/scf.t
4979
test_seqfeaturePrimer :: pure_all
4980
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/seqfeaturePrimer.t
4981
test_sequencetrace :: pure_all
4982
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/sequencetrace.t
4983
test_seqwithquality :: pure_all
4984
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/seqwithquality.t
4985
test_simpleGOparser :: pure_all
4986
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/simpleGOparser.t
4987
test_sirna :: pure_all
4988
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/sirna.t
4989
test_splicedseq :: pure_all
4990
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/splicedseq.t
4991
test_trim :: pure_all
4992
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/trim.t
4993
test_tutorial :: pure_all
4994
PERL_DL_NONLAZY=1 $(FULLPERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -e 'use Test::Harness qw(&runtests $$verbose); $$verbose=$(TEST_VERBOSE); runtests @ARGV;' t/tutorial.t
4995
4996
4997
4998
4999
5000
# End.
Loggerhead is a web-based interface for Breezy
Version: 2.0.1