[med-svn] r2638 - in trunk/packages/bioperl-run/trunk: . debian debian/patches
plessy at alioth.debian.org
plessy at alioth.debian.org
Sun Nov 9 15:08:38 UTC 2008
Author: plessy
Date: 2008-11-09 15:08:38 +0000 (Sun, 09 Nov 2008)
New Revision: 2638
Added:
trunk/packages/bioperl-run/trunk/debian/
trunk/packages/bioperl-run/trunk/debian/README.Debian
trunk/packages/bioperl-run/trunk/debian/changelog
trunk/packages/bioperl-run/trunk/debian/compat
trunk/packages/bioperl-run/trunk/debian/control
trunk/packages/bioperl-run/trunk/debian/copyright
trunk/packages/bioperl-run/trunk/debian/patches/
trunk/packages/bioperl-run/trunk/debian/patches/10-wrong-path-for-interpreter.patch
trunk/packages/bioperl-run/trunk/debian/patches/series
trunk/packages/bioperl-run/trunk/debian/rules
trunk/packages/bioperl-run/trunk/debian/watch
Log:
[svn-inject] Applying Debian modifications to trunk
Property changes on: trunk/packages/bioperl-run/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Added: trunk/packages/bioperl-run/trunk/debian/README.Debian
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/bioperl-run/trunk/debian/README.Debian 2008-11-09 15:08:38 UTC (rev 2638)
@@ -0,0 +1,36 @@
+bioperl-run for Debian
+----------------------
+
+(Extracted from the INSTALL file)
+
+ENVIRONMENT VARIABLES
+
+ Some important environment variables you need to be aware of.
+
+ Variable Values Comment
+ --------------------------------------------------------------------
+ PHYLIPVERSION 3.5, 3.6 If you want to run Phylip3.6 you
+ need to set this env variable to 3.6
+
+ BLASTDIR DIR PATH Point to the directory where BLAST
+ is installed
+
+ GENSCAN_DIR DIR PATH Point to the directory where
+ HumanIso.smat file is installed
+
+ EPONINEDIR DIR PATH Point to the directory where
+ eponine_scan.jar is installed
+
+ PAMLDIR DIR PATH Point to directory where PAML is
+ installed
+
+Generally the all-caps program name concatenated to 'DIR' patten for
+environment variable names is followed for most programs. However
+there are some exceptions (some require an underscore between the
+program name and 'DIR'), so check the documentation for the module
+you're interested in using.
+
+Note that for some programs, having the executables in your path is
+not enough - the correct environment variable still needs to be set,
+and sometimes it shouldn't point to the executable location, but
+somewhere else - again, check the documentation.
Added: trunk/packages/bioperl-run/trunk/debian/changelog
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/changelog (rev 0)
+++ trunk/packages/bioperl-run/trunk/debian/changelog 2008-11-09 15:08:38 UTC (rev 2638)
@@ -0,0 +1,5 @@
+bioperl-run (1.5.2.100-1) UNRELEASED; urgency=low
+
+ * Initial Release.
+
+ -- Charles Plessy <plessy at debian.org> Sun, 9 Nov 2008 21:26:48 +0900
Added: trunk/packages/bioperl-run/trunk/debian/compat
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/compat (rev 0)
+++ trunk/packages/bioperl-run/trunk/debian/compat 2008-11-09 15:08:38 UTC (rev 2638)
@@ -0,0 +1 @@
+7
Added: trunk/packages/bioperl-run/trunk/debian/control
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/control (rev 0)
+++ trunk/packages/bioperl-run/trunk/debian/control 2008-11-09 15:08:38 UTC (rev 2638)
@@ -0,0 +1,24 @@
+Source: bioperl-run
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 7), quilt, libmodule-build-perl
+Build-Depends-Indep: perl (>= 5.6.1)
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy at debian.org>
+Standards-Version: 3.8.0
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/bioperl-run/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/bioperl-run/trunk/
+Homepage: http://www.bioperl.org/wiki/Run_package
+
+Package: bioperl-run
+Architecture: all
+Depends: perl (>= 5.6.1), ${misc:Depends}, bioperl (>= 1.5.2)
+Suggests: emboss, hmmer, wise, molphy, phylip, clustalw, sim4, t-coffee, blast2, exonerate, amap
+Description: Wrapper modules for BioPerl
+ Contains modules that provide a Perl interface to various
+ bioinformatics applications to allow them to be
+ used with common BioPerl objects.
+ .
+ Not all the wrappable applications are packaged in Debian. The ones that are are
+ "Suggested" by this package.
Added: trunk/packages/bioperl-run/trunk/debian/copyright
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/copyright (rev 0)
+++ trunk/packages/bioperl-run/trunk/debian/copyright 2008-11-09 15:08:38 UTC (rev 2638)
@@ -0,0 +1,76 @@
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=311
+Upstream-Name: bioperl-run
+Upstream-Maintainer: Bioperl Team <bioperl-l at bioperl.org>
+Upstream-Source: http://bioperl.org/DIST/bioperl-run-1.5.2_100.tar.gz
+X-Packaged-By: Charles Plessy <plessy at debian.org>
+X-Packaged-Date: Sun, 09 Nov 2008 22:03:31 +0900
+
+Files: *
+Copyright: © 1997-2006 Bioperl Team <bioperl-l at bioperl.org>
+ Sendu Bala <bix at sendu.me.uk>
+ Jer-Ming Chia <giscjm at nus.edu.sg>
+ Rob Edwards <redwards at utmem.edu>
+ Mauricio Herrera Cuadra <arareko at campus.iztacala.unam.mx>
+ Shawn Hoon <shawnh at fugu-sg.org>
+ Donald Jackson <donald.jackson at bms.com>
+ Keith James <kdj at sanger.ac.uk>
+ Ratnapu Kiran Kumar <kiran at fugu-sg.org>
+ Balamurugan Kumarasamy <savikalpa at fugu-sg.org>
+ Catherine Letondal <letondal at pasteur.fr>
+ Heikki Lehvaslaiho <heikki at ebi.ac.uk>
+ Stephen Montgomery <smontgom at bcgsc.bc.ca>
+ Brian Osborne <bosborne at alum.mit.edu>
+ Tania Oh <gisoht at nus.edu.sg>
+ Peter Schattner <schattner at alum.mit.edu>
+ Martin Senger <senger at ebi.ac.uk>
+ Marc Sohrmann <ms2 at sanger.ac.uk>
+ Jason Stajich <jason at bioperl.org>
+ Elia Stupka <elia at fugu-sg.org>
+ David Vilanova <david.vilanova at urbanet.ch>
+ Albert Vilella <avilella at gmail.com>
+ Tiequan Zhang <tqzhang1973 at yahoo.com>
+ Juguang Xiao <juguang at tll.org.sg>
+License: Artistic | GPL-1+
+ Everyone can use it! We don't care if you are academic, corporate, or
+ government. BioPerl is licensed under the same terms as Perl itself, which
+ means it is dually-licensed under either the Artistic or GPL licenses. The Perl
+ Artistic License, or the GNU GPL covers all the legalese and what you can and
+ can't do with the source code.
+ .
+ We do appreciate:
+ .
+ * You letting us know you sell or use a product that uses BioPerl. This helps
+ us show people how useful our toolkit is. It also helps us if we seek funding
+ from a government source, to identify the utility of the code to many different
+ groups of users. Add your project and institution to our BioPerl Users page.
+ .
+ * If you fix bugs, please let us know about them. Because Bioperl is
+ dual-licensed under the GPL or Artistic licenses, you can choose the Artistic
+ license, which means that you are not required to submit the code fixes, but in
+ the spirit of making a better product we hope you'll contribute back to the
+ community any insight or code improvements.
+ .
+ * Please include the AUTHORS file and ascribe credit to the original BioPerl
+ toolkit where appropriate.
+ .
+ * If you are an academic and you use the software, please cite the article.
+ See the BioPerl publications for a list of papers which describe components in
+ the toolkit.
+X-Comment: see http://www.bioperl.org/wiki/Licensing_BioPerl
+X-Comment: Perl license
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of either:
+ .
+ a) the GNU General Public License as published by the Free Software
+ Foundation; either version 1, or (at your option) any later
+ version, or
+ .
+ b) the "Artistic License" which comes with Perl.
+X-Comment: On Debian systems, the complete text of the Artistic License can be
+ found in `/usr/share/common-licenses/Artistic', and the complete text of the
+ GNU General Public License can be found in `/usr/share/common-licenses/GPL'.
+
+Files: debian/*
+Copyright: © 2008 Charles Plessy <plessy at debian.org>
+License: Same as BioPerl itself
+ (see above)
Added: trunk/packages/bioperl-run/trunk/debian/patches/10-wrong-path-for-interpreter.patch
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/patches/10-wrong-path-for-interpreter.patch (rev 0)
+++ trunk/packages/bioperl-run/trunk/debian/patches/10-wrong-path-for-interpreter.patch 2008-11-09 15:08:38 UTC (rev 2638)
@@ -0,0 +1,24 @@
+Author: Charles Plessy
+Forwarded: http://bugzilla.open-bio.org/show_bug.cgi?id=2644
+Description: Corrects wrong path to Perl.
+License: same as BioPerl itself.
+diff --git a/Bio/Installer/Generic.pm b/Bio/Installer/Generic.pm
+index 5440566..f4b3070 100755
+--- a/Bio/Installer/Generic.pm
++++ b/Bio/Installer/Generic.pm
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ # BioPerl module for Bio::Installer::Generic
+ #
+diff --git a/Bio/Installer/PAML.pm b/Bio/Installer/PAML.pm
+index 6724af0..93dba5b 100755
+--- a/Bio/Installer/PAML.pm
++++ b/Bio/Installer/PAML.pm
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ # BioPerl module for Bio::Installer::PAML
+ #
Added: trunk/packages/bioperl-run/trunk/debian/patches/series
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/patches/series (rev 0)
+++ trunk/packages/bioperl-run/trunk/debian/patches/series 2008-11-09 15:08:38 UTC (rev 2638)
@@ -0,0 +1 @@
+10-wrong-path-for-interpreter.patch
Added: trunk/packages/bioperl-run/trunk/debian/rules
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/rules (rev 0)
+++ trunk/packages/bioperl-run/trunk/debian/rules 2008-11-09 15:08:38 UTC (rev 2638)
@@ -0,0 +1,71 @@
+#!/usr/bin/make -f
+# This debian/rules file is provided as a template for normal perl
+# packages. It was created by Marc Brockschmidt <marc at dch-faq.de> for
+# the Debian Perl Group (http://pkg-perl.alioth.debian.org/) but may
+# be used freely wherever it is useful.
+#
+# It was later modified by Jason Kohles <email at jasonkohles.com>
+# http://www.jasonkohles.com/ to support Module::Build installed modules
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+include /usr/share/quilt/quilt.make
+
+# If set to a true value then MakeMaker's prompt function will
+# always return the default without waiting for user input.
+export PERL_MM_USE_DEFAULT=1
+
+PERL ?= /usr/bin/perl
+PACKAGE = $(shell dh_listpackages)
+TMP = $(CURDIR)/debian/$(PACKAGE)
+
+build: patch build-stamp
+build-stamp:
+ dh_testdir
+ # Add commands to compile the package here
+ $(PERL) Build.PL installdirs=vendor
+ $(PERL) Build
+ # disabled tests because they depend on too much external programs
+ # $(PERL) Build test
+ touch $@
+
+clean: unpatch
+ dh_testdir
+ dh_testroot
+ dh_clean build-stamp install-stamp
+ # Add commands to clean up after the build process here
+ [ ! -f Build ] || $(PERL) Build --allow_mb_mismatch 1 distclean
+
+install: install-stamp
+install-stamp: build-stamp
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ # Add commands to install the package into $(TMP) here
+ $(PERL) Build install destdir=$(TMP) create_packlist=0
+ # prename is the rename utility written in perl usually available as /usr/bin/rename in Debian.
+ prename s/.pl$$// debian/bioperl-run/usr/bin/*pl
+ prename s/.pl.1p$$/.1p/ debian/bioperl-run/usr/share/man/man1/*1p
+ touch $@
+
+binary-arch:
+# We have nothing to do here for an architecture-independent package
+
+binary-indep: build install
+ dh_testdir
+ dh_testroot
+ dh_installdocs
+ dh_installexamples examples/*
+ chmod 644 debian/bioperl-run/usr/share/doc/bioperl-run/examples/pise/*
+ dh_installchangelogs Changes
+ dh_perl
+ dh_compress
+ dh_fixperms
+ dh_installdeb
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install
Property changes on: trunk/packages/bioperl-run/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/bioperl-run/trunk/debian/watch
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/watch (rev 0)
+++ trunk/packages/bioperl-run/trunk/debian/watch 2008-11-09 15:08:38 UTC (rev 2638)
@@ -0,0 +1,3 @@
+version=3
+#http://search.cpan.org/dist/bioperl-run/ .*/bioperl-run-v?(\d[\d_.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$
+http://www.bioperl.org/DIST/bioperl-run-([\d\.]+)_(\d*)\.tar\.gz
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