1
# $Id: INSTALL,v 1.28 2003/12/13 15:51:19 jason Exp $
3
Bioperl Install Directions
7
- Tested on all common forms of Unix, Win9X/NT/2000, Mac OS X
8
(see the PLATFORMS file for more details)
10
- perl 5.005 or later *.
12
- ANSI C or Gnu C compiler for optional extra XS extensions
14
- External modules: Bioperl uses functionality provided in other
15
Perl modules. Some of these are included in the standard perl
16
install and some need to be obtained from the CPAN (www.cpan.org)
17
site. The list of external modules is included at the bottom of
18
the INSTALL document and in the bptutorial.pl tutorial. The
19
Bioperl Bundle (Bundle::BioPerl) available through CPAN can make
20
this process even easier. Simply install the bundle in your CPAN
21
shell and all necessary modules will be installed.
23
- Bioperl on ActiveState for Windows - An ActiveState PPM distribution
24
is available for bioperl v. 1.0. Issue the following commands in
25
your PPM shell to install Bioperl (ActiveState Perl v. 5.6*).
27
PPM>repository add Bioperl http://bioperl.org/DIST/
29
Get the number of the Bioperl repository:
33
Set the Bioperl repository, find Bioperl, install Bioperl:
35
PPM>repository set <Bioperl repository number>
37
PPM>install <bioperl package number>
39
As of this writing the Bundle::BioPerl bundle is not found in any
40
ActiveState package but the following command should work in
43
>perl -MCPAN -e "install Bundle::BioPerl"
45
Do not use a Unix make to install Perl modules this way, use nmake.
46
See "DEPENDENCIES AND Bundle::BioPerl" below for more information
47
on this useful bundle.
49
- Additional information using Bioperl with MacOS can be
50
found at http://bioperl.org/Core/mac-bioperl.html
52
- Additional information using Bioperl with OS X can be
53
found at http://www.tc.umn.edu/~cann0010/Bioperl_OSX_install.html
56
Bioperl can interface with some external programs for executing
57
analyses. These include clustalw and t_coffee for Multiple
58
Sequence Alignments (Bio::Tools::Run::Alignment::Clustalw and
59
Bio::Tools::Run::TCoffee) and blastall,blastpgp, & bl2seq for BLAST
60
analyses (Bio::Tools::Run::StandAloneBlast), and to all the
61
programs in the EMBOSS suite (Bio::Factory::EMBOSS).
63
Additionally Bioperl can submit and retrieve jobs from the NCBI
64
Blast queue via the Bio::Tools::Run::RemoteBlast module.
66
See the documentation for these modules for more information
68
- Environment Variables
72
Some modules which run external programs need certain environment
73
variables set. If you do not have a local copy of the specific
74
executeable you do not need to set these variables. Additionally
75
the modules will attempt to locate the specific applications in
76
your runtime PATH variable. You may also need to set an environment
77
variable to tell BioPerl about your network configuration if your
80
Setting environment variables on unix means adding a line like the
81
following to your shell initialization:
83
(for bash,sh) export BLASTDIR=/data1/blast
84
(for csh,tcsh) setenv BLASTDIR /data1/blast
86
The environment variables include:
87
Bio::Tools::Run::StandAloneBlast
88
o BLASTDIR - which specifies where the NCBI blastall, blastpgp,
89
bl2seq, etc.. are located. A 'data' directory is
90
assumed to be present in this dir as well where the
91
blastable databases are located as well as
92
substitution matricies.
95
BLASTDB - (either is optional) if one does not want to locate the data dir
96
within the same dir as where the BLASTDIR variable
97
points, a BLASTDATADIR or BLASTDB variable can be set to
98
point to a dir where BLAST database indexes are located.
99
Bio::Tools::Run::Alignment::Clustalw
100
o CLUSTALDIR - points to the directory where the clustalw
101
executable is located.
102
Bio::Tools::Run::Alignment::TCoffee
103
o TCOFFEEDIR - points to the directory where the t_coffee
104
executable is located.
106
o HTTP_PROXY - If you access the internet via a proxy server then you
107
can tell the Bioperl modules which require network access
108
about this by using the HTTP_PROXY environment variable.
109
The value set includes the proxy address and the port
110
used (eg http://wwwcache.example.com:8080).
113
* Note that most modules will work with earlier versions of Perl.
114
The only ones that will not are Bio::SimpleAlign.pm and
115
the Bio::Index::* modules. If you don't need these modules
116
and you want to install bioperl using an earlier version of Perl,
117
edit the "require 5.004;" line in Makefile.PL as necessary.
123
The Bioperl modules are distributed as a tar file in standard perl
124
CPAN distribution form. This means that installation is very
125
simple. Once you have unpacked the tar distribution there is a
126
directory called bioperl-xx/, which is where this file is. Move into
127
that directory (you may well be already in the right place!) and
128
issue the following commands:
130
perl Makefile.PL # makes a system-specific makefile
131
make # makes the distribution
132
make test # runs the test code
133
make install # [may need root access for system install.
134
# See below for how to get around this.]
136
This should build, test and install the distribution cleanly on your
137
system. This installs the main perl part of bioperl, which is the
138
majority of the bioperl modules. There is one module (Bio::Tools::pSW)
139
which needs a compiled extension. This needs an extra installation
140
step. The directions for installing this are given below - it is
141
almost as easy as installing the standard distribution, so don't
144
You may have some errors from the pod2man part of the installation,
147
/usr/bin/pod2man: Unrecognized pod directive in paragraph 168 of Bio/Tools/Blast.pm: head3
149
You don't need to worry about them: they do not affect the documentation
152
To install you need write permission in the perl5/site_perl/ source area.
153
Quite often this will require you (or someone else) becoming root,
154
so you will want to talk to your systems manager if you don't
155
have the necessary access.
157
It is possible to install the package outside of the standard Perl5
158
location. See below for details.
160
To install the Compiled extension for pSW you will need to read the
161
next section of the manual.
164
INSTALLING THE OPTIONAL COMPILED EXTENSIONS (bioperl-ext package)
166
This Installation works out-of-the box for all platforms except *BSD
167
and Solaris boxes. For notes on this, read on. For other platforms,
168
skip ahead to the next section, BUILDING THE COMPILED EXTENSIONS.
170
INSTALLING for *BSD and Solaris boxes.
172
You should add the line -fPIC to the CFLAGS line in
173
Compile/SW/libs/makefile. This makes the compile generate position
174
independent code, which is required for these architectures. In
175
addition, on some Solaris boxes, the generated Makefile does not make
176
the correct -fPIC/-fpic flags for the C compiler that is used. This
177
requires manual editing of the generated Makefile to switch case. Try
178
it out once, and if you get errors, try editing the -fpic line
180
BUILDING THE COMPILED EXTENSIONS (OPTIONAL, ONLY FOR RUNNING LOCAL
181
PROTEIN SMITH-WATERMAN ANALYSES FROM PERL)
183
Move to the directory bioperl-ext. This is available as a separate
184
package released from ftp://bioperl.org/pub/DIST. This is where the C
185
code and XS extension for the bp_sw module is held and execute these
186
commands: (possibly after making the change for *BSD and Solaris, as
189
perl Makefile.PL # makes the system specific makefile
190
# Solaris/BSD users might need to edit the Makefile here
191
make # builds all the libaries
192
make test # runs a short test
193
make install # installs the package correctly.
195
This should install the compiled extension. The Bio::Tools::pSW module
196
will work cleanly now.
199
INSTALLING BIOPERL SCRIPTS
201
Bioperl comes with a set of production-quality scripts that are kept
202
in the scripts/ directory. You can install these scripts if you'd like,
203
simply follow the instructions on 'make install'. The installation
204
directory is specified by the INSTALLSCRIPT variable in the Makefile,
205
the default location is /usr/bin. Installation will copy the scripts
206
to the specified directory, change the 'PLS' suffix to 'pl', and
207
prepend 'bp_' to all the script names if they aren't so named already.
210
INSTALLING BIOPERL IN A PERSONAL OR PRIVATE MODULE AREA
212
If you lack permission to install perl modules into the
213
standard site_perl/ system area you can configure bioperl to
214
install itself anywhere you choose. Ideally this would
215
be a personal perl directory or standard place where you
216
plan to put all your 'local' or personal perl modules.
218
Note: you _must_ have write permission to this area.
220
Simply pass a parameter to perl as it builds your system
225
perl Makefile.PL LIB=/home/users/dag/My_Local_Perl_Modules
230
This tells perl to install bioperl in the desired place, e.g.:
232
/home/users/dag/My_Perl_Modules/Bio/Seq.pm
234
Then in your Bioperl script you would write:
236
use lib "/home/users/dag/My_Local_Perl_Modules";
239
The man pages will probably be installed in $LIB/man. For more
240
information on these sorts of custom installs see the documentation
241
for ExtUtils::MakeMaker.
243
See below for how to use modules that are not installed in the
244
standard Perl5 location.
246
You can also use CPAN, as discussed below, to install accessory modules
247
in your local directory. First enter the CPAN shell,
248
then set the arguments for the command "perl Makefile.PL":
1
# $Id: INSTALL,v 1.47.4.8 2006/12/06 18:20:15 sendu Exp $
3
Installing Bioperl for Unix
5
* 1 BIOPERL INSTALLATION
6
* 2 SYSTEM REQUIREMENTS
8
* 4 ADDITIONAL INSTALLATION INFORMATION
10
* 6 PRELIMINARY PREPARATION
11
* 7 INSTALLING BIOPERL THE EASY WAY USING CPAN
12
* 8 INSTALLING BIOPERL THE EASY WAY USING 'Build.PL'
13
* 9 WHERE ARE THE MAN PAGES?
14
* 10 EXTERNAL PROGRAMS
16
* 10.1 Environment Variables
18
* 11 INSTALLING BIOPERL SCRIPTS
19
* 12 INSTALLING BIOPERL IN A PERSONAL MODULE AREA
20
* 13 INSTALLING BIOPERL MODULES THE HARD WAY
21
* 14 USING MODULES NOT INSTALLED IN THE STANDARD LOCATION
23
* 16 BUILDING THE OPTIONAL bioperl-ext PACKAGE
25
* 16.1 CONFIGURING for BSD and Solaris boxes
30
Bioperl has been installed on many forms of Unix,
31
Win9X/NT/2000/XP, and on Mac OS X (see the PLATFORMS file for more
32
details). Following are instructions for installing Bioperl for
33
Unix/Linux/Mac OS X; Windows installation instructions can be found
34
in INSTALL.WIN. For installing Bioperl for Mac OS X using Fink, see:
36
http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink
40
* Perl 5.6.1 or later; version 5.8 and greater are recommended.
42
* External modules: Bioperl uses functionality provided in other
43
Perl modules. Some of these are included in the standard perl package
44
but some need to be obtained from the CPAN site. The list of external
45
modules is included in the DEPENDENCIES file.
49
* ANSI C or GNU C compiler (gcc) for XS extensions (the
50
bioperl-ext package; see BUILDING THE OPTIONAL bioperl-ext
53
ADDITIONAL INSTALLATION INFORMATION
55
* Additional information on Bioperl and MAC OS:
56
* OS 9 - http://bioperl.org/Core/mac-bioperl.html
57
* OS X - http://www.tc.umn.edu/~cann0010/Bioperl_OSX_install.html
58
(outdated, but useful for libgd installation notes)
59
* OS X - Installing using Fink (in Getting BioPerl)
63
Users of previous versions of Bioperl may remember Bundle::BioPerl.
64
You no longer need to install Bundle::BioPerl. Instead, the normal
65
installation process will ask you if you'd like to install the
66
optional external module dependencies that Bioperl has.
68
A full list of BioPerl dependencies can be found inf the DEPENDENCIES
69
file included with this distribution.
71
PRELIMINARY PREPARATION
73
This is optional, but regardless of your subsequent choice of installation
74
method, it will help to carry out the following steps. They will increase
75
the likelyhood of installation success (especially of optional
81
cpan>install Bundle::CPAN
84
* Install/upgrade Module::Build, and make it your preferred installer:
87
cpan>install Module::Build
88
cpan>o conf prefer_installer MB
92
* Install the expat and libgd libraries by whatever method is
93
appropriate for your system. If you install libgd in a non-standard
94
location, that is fine: when installing the perl module that needs it
95
you will be asked where you installed it.
97
* If your expat library is installed in a non-standard location, tell
101
cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib EXPATINCPATH=/non-standard/include"
104
INSTALLING BIOPERL THE EASY WAY USING CPAN
106
You can use the CPAN shell to install Bioperl. For example:
108
>perl -MCPAN -e shell
110
Or you might have the cpan alias installed:
114
Then find the name of the Bioperl version you want:
117
CPAN: Storable loaded ok
118
Going to read /home/bosborne/.cpan/Metadata
119
Database was generated on Mon, 20 Nov 2006 05:24:36 GMT
120
Distribution B/BI/BIRNEY/bioperl-1.2.tar.gz
121
Distribution B/BI/BIRNEY/bioperl-1.4.tar.gz
122
Distribution S/SE/SENDU/bioperl-1.5.2_100.tar.gz
126
cpan>install S/SE/SENDU/bioperl-1.5.2_100.tar.gz
128
If you've installed everything perfectly and all the network connections
129
are working then you may pass all the tests run in the './Build test' phase.
130
It's also possible that you may fail some tests. Possible explanations:
131
problems with local Perl installation, network problems, previously
132
undetected bug in Bioperl, flawed test script, problems with CGI
133
script used for sequence retrieval at public database, and so on. Remember
134
that there are over 800 modules in Bioperl and the test suite is running
135
more than 12000 individual tests, a few failed tests may not affect your
138
If you decide that the failed tests will not affect how you intend to use
139
Bioperl and you'd like to install anyway do:
141
cpan>force install S/SE/SENDU/bioperl-1.5.2_100.tar.gz
143
This is what most experienced Bioperl users would do. However, if you're
144
concerned about a failed test and need assistance or advice then contact
145
bioperl-l@bioperl.org.
147
INSTALLING BIOPERL THE EASY WAY USING Build.PL
149
The advantage of this approach is it's stepwise, so it's easy to stop and
150
analyze in case of any problem.
152
Download, then unpack the tar file. For example:
154
>gunzip bioperl-1.5.2_100.tar.gz
155
>tar xvf bioperl-1.5.2_100.tar
156
>cd bioperl-1.5.2_100
158
Now issue the build commands:
163
If you've installed everything perfectly and all the network connections
164
are working then you may pass all the tests run in the './Build test' phase.
165
It's also possible that you may fail some tests. Possible explanations:
166
problems with local Perl installation, network problems, previously
167
undetected bug in Bioperl, flawed test script, problems with CGI script
168
using for sequence retrieval at public database, and so on. Remember that
169
there are over 800 modules in Bioperl and the test suite is running more
170
than 12000 individual tests, a few failed tests may not affect your usage
173
If you decide that the failed tests will not affect how you intend to use
174
Bioperl and you'd like to install anyway, or if all tests were fine, do:
178
This is what most experienced Bioperl users would do. However, if you're
179
concerned about a failed test and need assistance or advice then contact
180
bioperl-l@bioperl.org.
182
To './Build install' you need write permission in the perl5/site_perl/source
183
area (or similar, depending on your environment). Usually this will require
184
you becoming root, so you will want to talk to your systems manager if you
185
don't have the necessary privileges.
187
It is also straightforward to install the package outside of the this
188
standard Perl5 location. See INSTALLING BIOPERL IN A PERSONAL MODULE
191
WHERE ARE THE MAN PAGES?
193
When using Makefile.PL (no longer covered in this documentation), we had
194
to disable the automatic creation of man pages because this step was
195
triggering a "line too long" error on some OSs due to shell constraints.
196
If you want man pages installed use the Build.PL installation process
201
Bioperl can interface with some external programs for executing analyses.
202
These include clustalw and t_coffee for Multiple Sequence Alignment
203
(Bio::Tools::Run::Alignment::Clustalw and
204
Bio::Tools::Run::Alignment::TCoffee) and blastall, blastpgp, and
205
bl2seq for BLAST analyses (Bio::Tools::Run::StandAloneBlast), and
206
to all the programs in the EMBOSS suite (Bio::Factory::EMBOSS).
208
Environment Variables
210
Some modules which run external programs need certain environment
211
variables set. If you do not have a local copy of the specific executable
212
you do not need to set these variables. Additionally the modules will
213
attempt to locate the specific applications in your runtime PATH variable.
214
You may also need to set an environment variable to tell BioPerl about
215
your network configuration if your site uses a firewall.
217
Setting environment variables on unix means adding lines like the
218
following to your shell *rc file.
222
export BLASTDIR=/data1/blast
226
setenv BLASTDIR /data1/blast
228
Some environment variables include:
230
+------------------------------------------------------------------------+
231
| Env. Variable | Description |
232
|---------------+--------------------------------------------------------|
233
| |Specifies where the NCBI blastall, blastpgp, bl2seq, |
234
|BLASTDIR |etc.. are located. A 'data' directory could also be |
235
| |present in this directory as well, you could put your |
236
| |blastable databases here. |
237
|---------------+--------------------------------------------------------|
238
| |If one does not want to locate the data dir within the |
239
|BLASTDATADIR or|same dir as where the BLASTDIR variable points, a |
240
|BLASTDB |BLASTDATADIR or BLASTDB variable can be set to point to |
241
| |a dir where BLAST database indexes are located. |
242
|---------------+--------------------------------------------------------|
243
|BLASTMAT |The directory containing the substitution matrices such |
245
|---------------+--------------------------------------------------------|
246
|CLUSTALDIR |The directory where the clustalw executable is located. |
247
|---------------+--------------------------------------------------------|
248
|TCOFFEEDIR |The directory where the t_coffee executable is located. |
249
|---------------+--------------------------------------------------------|
250
| |If you access the internet via a proxy server then you |
251
| |can tell the Bioperl modules which require network |
252
| |access about this by using the http_proxy environment |
253
|http_proxy |variable. The value set includes the proxy address and |
254
| |the port, with optional username/password for |
255
| |authentication purposes |
256
| |(e.g. http://USERNAME:PASSWORD@proxy.example.com:8080). |
257
+------------------------------------------------------------------------+
259
INSTALLING BIOPERL SCRIPTS
261
Bioperl comes with a set of production-quality scripts that are
262
kept in the scripts/ directory. You can install these scripts if you'd
263
like, simply answer the questions during 'perl Build.PL'.
264
The installation directory can be specified by:
267
./Build install --install_path script=/foo/scripts
269
By default they install to /usr/bin or similar, depending on platform.
271
INSTALLING BIOPERL IN A PERSONAL MODULE AREA
273
If you lack permission to install perl modules into the standard
274
site_perl/ system area you can configure Bioperl to install itself
275
anywhere you choose. Ideally this would be a personal perl directory or
276
standard place where you plan to put all your 'local' or personal perl
281
>perl Build.PL --install_base /home/users/dag
285
This tells perl to install all the various parts of bioperl in the desired
286
place, e.g. creating:
288
/home/users/dag/lib/perl5/Bio/Perl.pm
290
Then in your Bioperl script you would write:
292
use lib "/home/users/dag/lib/perl5/";
295
For more information on these sorts of custom installs see the documentation
298
If you are used to using something like:
300
>perl Makefile.PL PREFIX=/home/users/dag
302
You can get similar behaviour by using this instead:
304
>perl Build.PL --prefix /home/users/dag
306
For more information, see Module::Build::Cookbook documentation for
307
Installing_in_the_same_location_as_ExtUtils::MakeMaker
309
You can also use CPAN to install modules in your local directory. First
310
enter the CPAN shell, then set the arguments for the commands
311
"perl Makefile.PL" and "./Build install", like this:
250
313
>perl -e shell -MCPAN
251
314
cpan>o conf makepl_arg LIB=/home/users/dag/My_Local_Perl_Modules
256
INSTALLING BIOPERL MODULES: LAST RESORT
258
As a last resort, you can simply copy all files in Bio/
259
to any directory in which you have write privileges. This is
260
generally NOT recommended since some modules may require
261
special configuration (currently none do, but don't rely
264
You will need to set "use lib '/path/to/my/bioperl/modules';"
265
in your perl scripts so that you can access these modules if
266
they are not installed in the standard site_perl/ location.
267
See below for an example.
269
To get manpage documentation to work correctly you will have
270
to configure man so that it looks in the proper directory.
271
On most systems this will just involve adding an additional
272
directory to your $MANPATH environment variable.
274
The installation of the Compile directory can be similarly
275
redirected, but execute the make commands from the Compile/SW
278
If all else fails or are unable to access the perl distribution
279
directories, ask your system administrator to place the files there
280
for you. You can always execute perl scripts in the same directory
281
as the location of the modules (Bio/ in the distribution) since perl
282
always checks the current working directory when looking for modules.
285
USING MODULES NOT INSTALLED IN THE STANDARD PERL LOCATION
287
You can explicitly tell perl where to look for modules by using the
288
lib module which comes standard with perl.
294
use lib "/home/users/dag/My_Local_Perl_Modules/";
297
<...insert whizzy perl code here...>
299
Or, you can set the environmental variable PERL5LIB:
302
setenv PERL5LIB /home/users/dag/My_Local_Perl_Modules/
304
export PERL5LIB=/home/users/dag/My_Local_Perl_Modules/
309
The Bioperl test system is located in the t/ directory and is
310
automatically run whenever you execute the 'make test' command.
311
Alternatively if you want to investigate the behavior of a specific
312
test such as the SeqIO test you would type:
313
% perl -I. -w t/SeqIO.t
314
The -I tells Perl to use the current directory as the include path -
315
this makes sure you are testing the modules in this directory not
316
ones installed elsewhere in your PERL5LIB path.
317
The -w tells Perl to print all warnings.
319
If you are trying to learn how to use a module, often the test suite
320
is a good place to look. All good extreme programers try and write a
321
test BEFORE they write the module to insure that their module behaves
322
the way they expect. You'll notice some 'ok' and 'skip' commands in
323
a test, this is part of the Perl test suite that signifies a passed
324
test with an ok N where N is the test number. Alternatively you can
325
tell Perl to skip tests. This is useful when, for example, your test
326
detects that the network is not present and thus should skip, not
327
fail, any tests that require a network connection.
330
DEPENDENCIES AND Bundle::BioPerl
332
The following packages are used by Bioperl. Not all are required for
333
Bioperl to operate properly, however, some functionality will be
334
missing without them. You can easily install all of these, except
335
srsperl.pm, using the Bundle::BioPerl CPAN bundle. A command-line
338
>perl -e shell -MCPAN
339
cpan>install Bundle::BioPerl
340
<...installation details...>
345
>perl -MCPAN -e "install Bundle::BioPerl"
347
The DBD::mysql, DB_File and XML::Parser modules require other
348
applications or databases: MySQL, Berkeley DB, and expat respectively.
350
Module Where it is Used
351
------------------------------------------------------------------
352
HTTP::Request::Common GenBank+GenPept sequence retrieval,
353
remote http Blast jobs
355
Bio::Tools::Run::RemoteBlast
357
LWP::UserAgent GenBank+GenPept sequence retrieval,
358
remote http Blast jobs
360
Bio::Tools::Run::RemoteBlast
362
AcePerl Access to ACeDB databases
364
Available at http://stein.cshl.org
366
IO::String IO handle to read or write to a string
375
XML::Parser Parsing of XML documents
378
Bio::SearchIO::blastxml
379
Bio::Biblio::IO::medlinexml
381
http://sourceforge.net/projects/expat/
383
XML::Writer Parsing + writing of XML documents
387
XML::Parser::PerlSAX Parsing of XML documents
390
Bio::SearchIO::blastxml
391
Bio::Biblio::IO::medlinexml
393
XML::Twig Parsing of XML documents
394
Bio::Variation::IO::xml
396
File::Temp Temporary File creation
400
SOAP::Lite SOAP protocol, XEMBL Services
402
Bio::DB::XEMBLService
404
HTML::Parser HTML parsing of GDB page
407
DBD::mysql Mysql API for loading and querying of Mysql-based
408
GFF feature and BioSQL databases
410
bioperl-db external package
411
bioperl-pipeline external package
412
Mysql DB free from www.mysql.org
414
GD GD graphical drawing library
416
Requires GD library from www.boutell.com/gd
418
srsperl Sequence Retrieval System (SRS)
419
alternative way of retrieving
421
Bio::LiveSeq::IO::SRS.pm
422
See README in Bio/LiveSeq/IO
424
Storable Persistent object storage & retrieval
427
Text::Shellwords Text parser
428
Bio::Graphics::FeatureFile
433
DB_File Perl access to Berkeley DB
436
Bio::SeqFeature::Collection,
438
Requires Berkeley DB, from Linux RPM
439
or from www.sleepycat.com
441
Graph::Directed generic graph data and algorithms
442
Bio::Ontology::SimpleOntologyEngine
444
Data::Stag::ITextWriter Structured Tags datastructures
445
Bio::SeqIO::chadoitext
447
Data::Stag::SxprWriter Structured Tags datastructures
448
Bio::SeqIO::chadosxpr
450
Data::Stag::XMLWriter Structured Tags datastructures
452
Text::Wrap (Very optional)
453
Bio::SearchIO::Writer::TextResultWriter
454
HTML::Entities (only if you want to run webanalysis modules)
455
Bio::Tools::Analysis::DNA::*
456
Bio::Tools::Analysis::Protein::*
315
cpan>o conf mbuild_install_arg "--install_path lib=/home/users/dag/My_Local_Perl_Modules"
318
INSTALLING BIOPERL MODULES THE HARD WAY
320
As a last resort, you can simply copy all files in Bio/ to any directory
321
in which you have write privileges. This is generally NOT recommended
322
since some modules may require special configuration (currently none do,
323
but don't rely on this).
325
You will need to set "use lib '/path/to/my/bioperl/modules';" in your perl
326
scripts so that you can access these modules if they are not installed in
327
the standard site_perl/ location. See above for an example.
329
To get manpage documentation to work correctly you will have to
330
configure man so that it looks in the proper directory. On most systems
331
this will just involve adding an additional directory to your $MANPATH
332
environment variable.
334
The installation of the Compile directory can be similarly redirected, but
335
execute the make commands from the Compile/SW directory.
337
If all else fails and you are unable to access the perl distribution
338
directories, ask your system administrator to place the files there for
339
you. You can always execute perl scripts in the same directory as the
340
location of the modules (Bio/ in the distribution) since perl always
341
checks the current working directory when looking for modules.
343
USING MODULES NOT INSTALLED IN THE STANDARD LOCATION
345
You can explicitly tell perl where to look for modules by using the
346
Lib module which comes standard with perl.
351
use lib "/home/users/dag/lib/perl5/";
353
#<...insert whizzy perl code here...>
355
Or, you can set the environmental variable PERL5LIB:
359
setenv PERL5LIB /home/users/dag/lib/perl5/
363
export PERL5LIB=/home/users/dag/lib/perl5/
367
The Bioperl test system is located in the t/ directory and is
368
automatically run whenever you execute the './Build test' command
369
(having previously run 'Perl Build.PL'; if you have already installed
370
Bioperl answer 'no' to script installation to get nicer test output
372
Alternatively if you want to investigate the behavior of a specific test
373
such as the Seq test you would type:
375
>./Build test --test_files t/Seq.t --verbose
377
The ./ ensures you are using the Build script in the current directory to
378
make sure you are testing the modules in this directory not ones
379
installed elsewhere. The --test_files arguement can be used multiple times
380
to try a set of test scripts in one go. The --verbose arguement outputs
381
the detailed test results, instead of just the summary you see during
384
If you are trying to learn how to use a module, often the test suite is a
385
good place to look. All good extreme programmers try and write a test
386
BEFORE they write the module to insure that their module behaves the way
387
they expect. You'll notice some 'ok' and 'skip' commands in a test, this
388
is part of the Perl test suite that signifies a passed test with an 'ok
389
N', where N is the test number. Alternatively you can tell Perl to skip
390
tests. This is useful when, for example, your test detects that the
391
network is not present and thus should skip, not fail, any tests that
392
require a network connection.
394
BUILDING THE OPTIONAL bioperl-ext PACKAGE
396
The bioperl-ext package contains C code and XS extensions for
397
various alignment and trace file modules (Bio::Tools::pSW for DNA
398
Smith-Waterman, Bio::Tools::dpAlign for protein Smith-Waterman,
399
Bio::SearchDist for EVD fitting of extreme value,
402
This Installation may work out-of-the box for most platforms except BSD
403
and Solaris boxes. For other platforms skip this next paragraph. Of note,
404
the code for bioperl-ext has not been updated along with the rest of bioperl,
405
so one may expect to see some issues. If so, please report them to the
406
BioPerl mailing list.
408
CONFIGURING for BSD and Solaris boxes
410
You should add the line -fPIC to the CFLAGS line in
411
Compile/SW/libs/makefile. This makes the compile generate position
412
independent code, which is required for these architectures. In addition,
413
on some Solaris boxes, the generated Makefile does not make the correct
414
-fPIC/-fpic flags for the C compiler that is used. This requires manual
415
editing of the generated Makefile to switch case. Try it out once, and if
416
you get errors, try editing the -fpic line
420
Move to the directory bioperl-ext. This is available as a separate package
421
released from ftp://bioperl.org/pub/bioperl/DIST. This is where the C
422
code and XS extension for the bp_sw module is held and execute these
423
commands: (possibly after making the change for BSD and Solaris, as
426
perl Makefile.PL # makes the system specific makefile
427
make # builds all the libaries
428
make test # runs a short test
429
make install # installs the package correctly.
431
This should install the compiled extension. The Bio::Tools::pSW
432
module will work cleanly now.
added
removed
INSTALL
