Commit cecd7da3 authored by Charles Plessy's avatar Charles Plessy

[svn-inject] Applying Debian modifications to trunk

parent 7936a683
bioperl-run for Debian
(Extracted from the INSTALL file)
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
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.
bioperl-run ( UNRELEASED; urgency=low
* Initial Release.
-- Charles Plessy <> Sun, 9 Nov 2008 21:26:48 +0900
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 <>
DM-Upload-Allowed: yes
Uploaders: Charles Plessy <>
Standards-Version: 3.8.0
Vcs-Svn: svn://
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.
Upstream-Name: bioperl-run
Upstream-Maintainer: Bioperl Team <>
X-Packaged-By: Charles Plessy <>
X-Packaged-Date: Sun, 09 Nov 2008 22:03:31 +0900
Files: *
Copyright: © 1997-2006 Bioperl Team <>
Sendu Bala <bix at>
Jer-Ming Chia <giscjm at>
Rob Edwards <redwards at>
Mauricio Herrera Cuadra <arareko at>
Shawn Hoon <shawnh at>
Donald Jackson <donald.jackson at>
Keith James <kdj at>
Ratnapu Kiran Kumar <kiran at>
Balamurugan Kumarasamy <savikalpa at>
Catherine Letondal <letondal at>
Heikki Lehvaslaiho <heikki at>
Stephen Montgomery <smontgom at>
Brian Osborne <bosborne at>
Tania Oh <gisoht at>
Peter Schattner <schattner at>
Martin Senger <senger at>
Marc Sohrmann <ms2 at>
Jason Stajich <jason at>
Elia Stupka <elia at>
David Vilanova <david.vilanova at>
Albert Vilella <avilella at>
Tiequan Zhang <tqzhang1973 at>
Juguang Xiao <juguang at>
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
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 <>
License: Same as BioPerl itself
(see above)
Author: Charles Plessy
Description: Corrects wrong path to Perl.
License: same as BioPerl itself.
diff --git a/Bio/Installer/ b/Bio/Installer/
index 5440566..f4b3070 100755
--- a/Bio/Installer/
+++ b/Bio/Installer/
@@ -1,4 +1,4 @@
# BioPerl module for Bio::Installer::Generic
diff --git a/Bio/Installer/ b/Bio/Installer/
index 6724af0..93dba5b 100755
--- a/Bio/Installer/
+++ b/Bio/Installer/
@@ -1,4 +1,4 @@
# BioPerl module for Bio::Installer::PAML
#!/usr/bin/make -f
# This debian/rules file is provided as a template for normal perl
# packages. It was created by Marc Brockschmidt <> for
# the Debian Perl Group ( but may
# be used freely wherever it is useful.
# It was later modified by Jason Kohles <>
# 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.
PERL ?= /usr/bin/perl
PACKAGE = $(shell dh_listpackages)
TMP = $(CURDIR)/debian/$(PACKAGE)
build: patch build-stamp
# 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_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_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 $@
# We have nothing to do here for an architecture-independent package
binary-indep: build install
dh_installexamples examples/*
chmod 644 debian/bioperl-run/usr/share/doc/bioperl-run/examples/pise/*
dh_installchangelogs Changes
binary: binary-indep binary-arch
.PHONY: build clean binary-indep binary-arch binary install
# .*/bioperl-run-v?(\d[\d_.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$[\d\.]+)_(\d*)\.tar\.gz
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