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GNU Source Release Collection (GSRC)
####################################
Introduction
------------
The GNU Source Release Collection provides a simple way to install the
latest GNU packages (and more) in their own directory (on an existing system).
This is particularly useful when you want to install them on
a system for which you do not have administrative rights, such as a
shared cluster. It simplifies the process of maintaining a collection
of locally installed software by cleanly separating the files of each
package (and each package version), and installing symbolic links to
the files in the directory of your choice.
Bioinformatics Source Release Collection is
now part of GNU Source Release Collection GSRC.
### Getting started
First, get it.
bzr checkout bzr://bzr.savannah.gnu.org/gsrc/trunk/ gsrc
( or download a tar file from ftp://ftp.gnu.org/gnu, but
bzr method will bring up-to-date files, which change daily.)
To get started, you must first configure it. From a shell, type:
$ ./bootstrap
$ ./configure --prefix=$HOME/gnu
You may choose to install the GNU software to any location you like by
setting the `--prefix' argument (they will be installed to ~/gnu in
the above example).
To update, in the gsrc directory, just do:
bzr update
You will find the available GNU packages under the `gnu'
sub-directory. Since they encompass a large number of packages in
their own right, the GNUstep and GNOME projects have their own
sub-directories: `gnustep' and `gnome', respectively.
Also 'bio' for bioinformatics, and 'other' for whatever else.
To get help on getting started, type "make help".
Status
------
For a complete listing of packages and their current status in GSRC,
see https://www.gnu.org/software/gsrc/package-list.html
Bugs and build failures
-----------------------
If you encounter a package that does not build properly, please first
check its status in `TODO'; there are a few packages which are known to
not build properly. If the affected package is listed as `DONE' and
not `BROKEN', then this should be reported. Similarly, if you find any
outdated packages, please report them. All problems can be sent to the
GSRC bug mailing list <bug-gsrc@gnu.org>.
## Featured software
If a program is missing from GSRC or BioSRC, please send a message to the
mailing list bug-gsrc@gnu.org to request its addition.
Similarly, if you notice that a program version is out-of-date, please
send a message.
Only software that is licensed under an accepted free software license
will be included in GSRC/BioSRC. Lamentably, many bioinformatics programs
are released in binary format only, under proprietary licenses, under
otherwise restrictive licenses ("...for academic use only...") or,
just as bad, with no explicit license at all (which effectively makes
the software proprietary). Distributing binary-only files is
tantamount to hiding your scientific methods, while restrictive,
proprietary licenses undermine the principles of open and
collaborative science. Thus, the use of such programs should not be
encouraged. Finally, anyone installing software with BioSRC should be
confident that they have full permission to use the software in any
way they like. We don't want to provide software that not everyone
can use! If you wish to have a program added to BioSRC that is
proprietary or under a restrictive license, please contact the
software's author(s) to encourage them to re-release the software
under an appropriate license.
## Supported systems
GSCR/BioSRC is geared towards installing software on GNU/Linux systems.
It may be possible to use it on other Unix-oid operating systems,
however note that you might need to modify some files to make them work.
Patches to support building on other systems will only be accepted if
they do not disrupt building on GNU/Linux systems.
Windows? You might have some luck with CygWin, but no support can be
given in that regard.
Copying
-------
GSRC is based on the GAR build system by Nick Moffitt and GARstow
enhancements by Adam Sampson.
Files from GAR and GARstow are under the following license unless
otherwise noted:
Copyright (C) 2001 Nick Moffitt
Copyright (C) 2004, 2005, 2006, 2007, 2008, 2009, 2010 Adam Sampson
Redistribution and/or use, with or without modification, is
permitted. This software is without warranty of any kind. The
author(s) shall not be liable in the event that use of the
software causes damage.
Files specific to GSRC, including the build recipes, are Copyright (C)
Free Software Foundation and licensed under the GNU General Public
License, Version 3, or (at your option) any later version. Please see
the file `COPYING' for more information.
<!-- Copyright (C) 2014 Brandon Invergo <brandon@invergo.net> -->
<!-- Author: Brandon Invergo <brandon@invergo.net> -->
<!-- This program is free software; you can redistribute it and/or -->
<!-- modify it under the terms of the GNU General Public License -->
<!-- as published by the Free Software Foundation; either version 3 -->
<!-- of the License, or (at your option) any later version. -->
<!-- This program is distributed in the hope that it will be useful, -->
<!-- but WITHOUT ANY WARRANTY; without even the implied warranty of -->
<!-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -->
<!-- GNU General Public License for more details. -->
<!-- You should have received a copy of the GNU General Public License -->
<!-- along with this program. If not, see <http://www.gnu.org/licenses/>. -->
## Copying
BioSRC is based on the GNU Source Release Collection (GSRC), which is
in turn based on the GAR build system by Nick Moffitt and GARstow
enhancements by Adam Sampson.
Files specific to BioSRC, including the build recipes, are Copyright
(C) Brandon Invergo and licensed under the GNU General Public License,
Version 3, or (at your option) any later version. Please see the file
`COPYING` for more information.
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