[med-svn] r312 - in trunk/packages/bioperl/trunk: . debian
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Thu Jun 14 23:46:15 UTC 2007
Author: charles-guest
Date: 2007-06-14 23:46:14 +0000 (Thu, 14 Jun 2007)
New Revision: 312
Added:
trunk/packages/bioperl/trunk/debian/
trunk/packages/bioperl/trunk/debian/README.Debian
trunk/packages/bioperl/trunk/debian/changelog
trunk/packages/bioperl/trunk/debian/compat
trunk/packages/bioperl/trunk/debian/control
trunk/packages/bioperl/trunk/debian/copyright
trunk/packages/bioperl/trunk/debian/dirs
trunk/packages/bioperl/trunk/debian/docs
trunk/packages/bioperl/trunk/debian/rules
trunk/packages/bioperl/trunk/debian/watch
trunk/packages/bioperl/trunk/test.swiss
Modified:
trunk/packages/bioperl/trunk/Build.PL
Log:
[svn-inject] Applying Debian modifications to trunk
Modified: trunk/packages/bioperl/trunk/Build.PL
===================================================================
--- trunk/packages/bioperl/trunk/Build.PL 2007-06-14 23:44:47 UTC (rev 311)
+++ trunk/packages/bioperl/trunk/Build.PL 2007-06-14 23:46:14 UTC (rev 312)
@@ -32,7 +32,7 @@
'Test::More' => 0,
'Module::Build' => 0.2805,
'Test::Harness' => 2.62,
- 'CPAN' => 1.81
+ #'CPAN' => 1.81
},
recommends => { # does what you would expect of recommends, except more informative output and generates optional_features in META.yml
'Ace' => '0/access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace',
Added: trunk/packages/bioperl/trunk/debian/README.Debian
===================================================================
--- trunk/packages/bioperl/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/bioperl/trunk/debian/README.Debian 2007-06-14 23:46:14 UTC (rev 312)
@@ -0,0 +1,10 @@
+bioperl for DEBIAN
+----------------------
+
+BioPerl on Debian has been configured to use the readseq program
+(see Bio::Parse and Bio::Seq) and so depends on readseq.
+
+Stephane Bortzmeyer <bortzmeyer at debian.org>, Wed, 19 May 1999 11:35:30 +0200
+
+Adopted by a new maintainer
+ Matt Hope <dopey at debian.org> Tue, 6 Nov 2001 17:17:30 +1100
Added: trunk/packages/bioperl/trunk/debian/changelog
===================================================================
--- trunk/packages/bioperl/trunk/debian/changelog (rev 0)
+++ trunk/packages/bioperl/trunk/debian/changelog 2007-06-14 23:46:14 UTC (rev 312)
@@ -0,0 +1,115 @@
+bioperl (1.5.2-1) experimental; urgency=low
+
+ * Developper release.
+ * Upgraded source package to debhelper 5 and standards-version 3.7.2.
+ * Added libmodule-build-perl and libtest-harness-perl to
+ build-depends-indep.
+ * Disabled automatic CRAN downolad.
+ * Updated Recommends list for the binary package.
+ * Moved the "production-quality" scripts to /usr/bin/.
+ * New maintainer: Debian-Med packaging team mailing list.
+ * New uploader: Charles Plessy.
+ * Updated Depends, Recommends and Suggests.
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Thu, 14 Jun 2007 20:41:25 +0900
+
+bioperl (1.4-1) unstable; urgency=low
+
+ * New upstream release
+ * Examples and working code are installed by default to usr/bin,
+ this has been moved to usr/share/doc/bioperl/bin
+
+ -- Matt Hope <matth at bioinformatics.unsw.edu.au> Sun, 18 Apr 2004 14:24:11 +1000
+
+bioperl (1.2.1-2) unstable; urgency=low
+
+ * Updated dependancies to libgd-gd2-perl
+ (Closes: Bug#192210)
+ * Same maintainer, different email address
+
+ -- Matt Hope <matth at bioinformatics.unsw.edu.au> Mon, 30 Jun 2003 23:40:59 +1000
+
+bioperl (1.2.1-1) unstable; urgency=low
+
+ * New upstream release
+ * Added more Depends/Reconmends.
+ * Added Depend: libio-string-perl
+ (Closes: Bug#188395)
+
+ -- Matt Hope <dopey at debian.org> Sat, 3 May 2003 01:21:54 +1000
+
+bioperl (1.2-1) unstable; urgency=low
+
+ * New upstream release
+
+ -- Matt Hope <dopey at debian.org> Fri, 25 Apr 2003 12:30:10 +1000
+
+bioperl (1.0.2-1) unstable; urgency=low
+
+ * *Another* new upstream release.
+
+ -- Matt Hope <dopey at debian.org> Wed, 17 Jul 2002 09:58:09 +1000
+
+bioperl (1.0.1-1) unstable; urgency=low
+
+ * New upstream release
+
+ -- Matt Hope <dopey at debian.org> Sat, 29 Jun 2002 22:35:08 +1000
+
+bioperl (1.0-1) unstable; urgency=low
+
+ * New upstream release
+
+ -- Matt Hope <dopey at debian.org> Wed, 20 Mar 2002 01:16:30 +1100
+
+bioperl (0.7.2-1) unstable; urgency=low
+
+ * New upstream release.
+ * Adopted by new maintainer; closes: #100208
+ * Fixed lintian errors.
+
+ -- Matt Hope <dopey at quickstix.com.au> Thu, 22 Nov 2001 19:31:26 +1100
+
+bioperl (0.7.1-1) unstable; urgency=low
+
+ * Maintainer set to Debian QA Group <packages at qa.debian.org>.
+ * New upstream release.
+
+ -- Adrian Bunk <bunk at fs.tum.de> Fri, 24 Aug 2001 20:47:57 +0200
+
+bioperl (0.7.0-1) unstable; urgency=low
+
+ * New upstream release; closes: #44245
+
+ -- Dr. Guenter Bechly <gbechly at debian.org> Sat, 5 May 2001 18:35:44 +0200
+
+bioperl (0.05.1-3) unstable; urgency=low
+
+ * Fixed compliance with perl policy; closes: #95880, #95418
+
+ -- Dr. Guenter Bechly <gbechly at debian.org> Tue, 1 May 2001 08:13:09 +0200
+
+bioperl (0.05.1-2) unstable; urgency=low
+
+ * Adopted by new maintainer; closes: #92806
+ * Updated to latest standards version and added Build-Depends (changed
+ control, copyright, dirs, docs, and rules);
+ closes: #70154, #91121, #91397
+ * Fixed some lintian errors in rules.
+ * Moved package to section non-free/science, because it is a tool that
+ is exclusively useful for molecular biologists.
+
+ -- Dr. Guenter Bechly <gbechly at debian.org> Fri, 20 Apr 2001 19:48:05 +0200
+
+bioperl (0.05.1-1) unstable; urgency=low
+
+ * Complies with the new Perl policy. Closes #40564
+ * New upstream release
+
+ -- Stephane Bortzmeyer <bortzmeyer at debian.org> Wed, 7 Jul 1999 14:49:16 +0200
+
+bioperl (0.05-1) unstable; urgency=low
+
+ * Initial Release.
+
+ -- Stephane Bortzmeyer <bortzmeyer at debian.org> Wed, 19 May 1999 11:35:30 +0200
Added: trunk/packages/bioperl/trunk/debian/compat
===================================================================
--- trunk/packages/bioperl/trunk/debian/compat (rev 0)
+++ trunk/packages/bioperl/trunk/debian/compat 2007-06-14 23:46:14 UTC (rev 312)
@@ -0,0 +1 @@
+5
Added: trunk/packages/bioperl/trunk/debian/control
===================================================================
--- trunk/packages/bioperl/trunk/debian/control (rev 0)
+++ trunk/packages/bioperl/trunk/debian/control 2007-06-14 23:46:14 UTC (rev 312)
@@ -0,0 +1,19 @@
+Source: bioperl
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Charles Plessy <charles-debian-nospam at plessy.org>
+Build-Depends: debhelper (>= 5), perl (>= 5.6.1), libmodule-build-perl (>= 0.2805), libtest-harness-perl (>= 2.62)
+Standards-Version: 3.7.2
+
+Package: bioperl
+Architecture: all
+Depends: libio-string-perl, ${perl:Depends}
+Recommends: libace-perl, libbio-asn1-entrezgene-perl, libclass-autoclass-perl, libclone-perl, libconvert-binary-c-perl, libdata-stag-xmlwriter-perl, libgd-gd2-perl, libgraph-perl, libhtml-parser-perl, libwww-perl, libpostscript-textblock-perl, libset-scalar-perl, libsoap-lite-perl, libspreadsheet-parseexcel-perl, libsvg-perl, libsvg-graph-perl, libtext-shellwords-perl, liburi-perl, libxml-parser-perl, libxml-perl, libxml-sax-perl, libxml-sax-writer-perl, libxml-twig-perl, libxml-writer-perl, libdbd-mysql-perl
+Suggests: blast2, clustalw, emboss, primer3, repeatmasker, glimmer, hmmer, molphy, phylip, sim4 | sibsim4, wise, exonerate,
+Description: Perl tools for computational molecular biology
+ The Bioperl project is a coordinated effort to collect computational methods
+ routinely used in bioinformatics into a set of standard CPAN-style,
+ well-documented, and freely available Perl modules.
+ .
+ Homepage: http://www.bioperl.org/
Added: trunk/packages/bioperl/trunk/debian/copyright
===================================================================
--- trunk/packages/bioperl/trunk/debian/copyright (rev 0)
+++ trunk/packages/bioperl/trunk/debian/copyright 2007-06-14 23:46:14 UTC (rev 312)
@@ -0,0 +1,15 @@
+This package was debianized by Stephane Bortzmeyer bortzmeyer at debian.org on
+Wed, 19 May 1999 11:35:30 +0200.
+
+It was downloaded from <http://bio.perl.org/>, the reference site.
+
+Upstream Authors: Many. Contact address is
+<vsns-bcd-perl-guts at lists.uni-bielefeld.de> or
+<bioperl-bugs at bio.perl.org> for the bugs.
+
+Copyright: Artistic
+
+You are free to distribute this software under the terms of
+the Artistic Licence.
+On Debian systems, the complete text of the Artistic
+Licence can be found in /usr/share/common-licenses/Artistic file.
Added: trunk/packages/bioperl/trunk/debian/dirs
===================================================================
--- trunk/packages/bioperl/trunk/debian/dirs (rev 0)
+++ trunk/packages/bioperl/trunk/debian/dirs 2007-06-14 23:46:14 UTC (rev 312)
@@ -0,0 +1 @@
+usr/share/perl5
Added: trunk/packages/bioperl/trunk/debian/docs
===================================================================
--- trunk/packages/bioperl/trunk/debian/docs (rev 0)
+++ trunk/packages/bioperl/trunk/debian/docs 2007-06-14 23:46:14 UTC (rev 312)
@@ -0,0 +1,4 @@
+README
+DEPRECATED
+BUGS
+AUTHORS
Added: trunk/packages/bioperl/trunk/debian/rules
===================================================================
--- trunk/packages/bioperl/trunk/debian/rules (rev 0)
+++ trunk/packages/bioperl/trunk/debian/rules 2007-06-14 23:46:14 UTC (rev 312)
@@ -0,0 +1,71 @@
+#!/usr/bin/make -f
+
+build: build-stamp
+build-stamp:
+ dh_testdir
+ echo "n" | perl Makefile.PL INSTALLDIRS=vendor
+ $(MAKE) OPTIMIZE="-O2 -g -Wall"
+ touch build-stamp
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp install-stamp
+
+ -if [ -f Makefile ]; then $(MAKE) realclean ; fi
+ -rm -f biodatabases.pod biodesign.pod bioperl.pod bioscripts.pod
+ -rm -f bioperl.conf
+
+ dh_clean
+
+install: install-stamp
+install-stamp: build-stamp
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+
+ # Add here commands to install the package into debian/bioperl.
+ $(MAKE) install PREFIX=`pwd`/debian/bioperl/usr INSTALLMAN3DIR=`pwd`/debian/bioperl/usr/share/man/man3
+# rm -f debian/bioperl/usr/lib/perl5/*-linux/*/perllocal.pod
+# rm -f debian/bioperl/usr/lib/perl/5.6.0/perllocal.pod
+ find debian/bioperl -type f -name .packlist | xargs rm -f
+# -find debian/bioperl/usr/lib/ -depth -type d -empty | xargs rmdir
+# -chmod a-x debian/bioperl/usr/share/perl5/*.pod
+# chmod 644 debian/bioperl/usr/share/perl5/Bio/Variation/README
+# chmod 644 debian/bioperl/usr/share/perl5/Bio/Tools/BPlite/Iteration.pm
+# chmod 644 debian/bioperl/usr/share/perl5/Bio/Tools/BPpsilite.pm
+# find debian/bioperl/usr/share/perl5/Bio -type f -exec chmod a-x {} \;
+#X# chmod 644 debian/bioperl/usr/share/perl5/Bio/Tools/Blast/Run/Makefile.PL
+# chmod 644 debian/bioperl/usr/share/perl5/Bio/Tools/Blast/CHANGES
+# chmod 644 debian/bioperl/usr/share/perl5/Bio/Tools/Blast/README
+
+# -mv debian/bioperl/usr/share/perl5/bptutorial.pl debian/bioperl/usr/share/doc/bioperl/examples/
+
+ rename s/.pl$$// debian/bioperl/usr/bin/*pl
+ rename s/.pl.1p$$/.1p/ debian/bioperl/usr/share/man/man1/*1p
+
+ touch install-stamp
+
+binary-indep: build install
+
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+# chmod a-x -R debian/bioperl/usr/share/doc/bioperl/examples
+ dh_installchangelogs Changes
+ dh_installdocs
+ dh_installexamples examples/*
+ dh_install
+ dh_installman
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_perl
+ dh_installdeb
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary
Property changes on: trunk/packages/bioperl/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/bioperl/trunk/debian/watch
===================================================================
--- trunk/packages/bioperl/trunk/debian/watch (rev 0)
+++ trunk/packages/bioperl/trunk/debian/watch 2007-06-14 23:46:14 UTC (rev 312)
@@ -0,0 +1,2 @@
+version=2
+http://www.bioperl.org/DIST/ bioperl-([0-9\.]*)\.tar\.gz debian uupdate
Added: trunk/packages/bioperl/trunk/test.swiss
===================================================================
--- trunk/packages/bioperl/trunk/test.swiss (rev 0)
+++ trunk/packages/bioperl/trunk/test.swiss 2007-06-14 23:46:14 UTC (rev 312)
@@ -0,0 +1,57 @@
+ID GCDH_CAEEL STANDARD; PRT; 409 AA.
+AC Q20772;
+DT 01-NOV-1997 (Rel. 35, Created)
+DT 01-NOV-1997 (Rel. 35, Last sequence update)
+DT 16-OCT-2001 (Rel. 40, Last annotation update)
+DE PROBABLE GLUTARYL-COA DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.3.99.7)
+DE (GCD).
+GN F54D5.7.
+OS Caenorhabditis elegans.
+OC Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea;
+OC Rhabditidae; Peloderinae; Caenorhabditis.
+OX NCBI_TaxID=6239;
+RN [1]
+RP SEQUENCE FROM N.A.
+RC STRAIN=BRISTOL N2;
+RA Coles L.;
+RT
+RL Submitted (OCT-1995) to the EMBL/GenBank/DDBJ databases.
+CC -!- CATALYTIC ACTIVITY: GLUTARYL-COA + ACCEPTOR = CROTONOYL-COA +
+CC CO(2) + REDUCED ACCEPTOR.
+CC -!- COFACTOR: FAD (BY SIMILARITY).
+CC -!- PATHWAY: DEGRADATIVE PATHWAY OF L-LYSINE, L-HYDROXYLYSINE,
+CC AND L-TRYPTOPHAN METABOLISM.
+CC -!- SUBCELLULAR LOCATION: MITOCHONDRIAL MATRIX (POTENTIAL).
+CC -!- SIMILARITY: BELONGS TO THE ACYL-COA DEHYDROGENASES FAMILY.
+CC --------------------------------------------------------------------------
+CC This SWISS-PROT entry is copyright. It is produced through a collaboration
+CC between the Swiss Institute of Bioinformatics and the EMBL outstation -
+CC the European Bioinformatics Institute. There are no restrictions on its
+CC use by non-profit institutions as long as its content is in no way
+CC modified and this statement is not removed. Usage by and for commercial
+CC entities requires a license agreement (See http://www.isb-sib.ch/announce/
+CC or send an email to license at isb-sib.ch).
+CC --------------------------------------------------------------------------
+DR EMBL; Z66513; CAA91333.1; -.
+DR HSSP; Q06319; 1BUC.
+DR WormPep; F54D5.7; CE03411.
+DR InterPro; IPR001552; Acyl-CoA_dh.
+DR Pfam; PF00441; Acyl-CoA_dh; 1.
+DR Pfam; PF02770; Acyl-CoA_dh_M; 1.
+DR Pfam; PF02771; Acyl-CoA_dh_N; 1.
+DR PROSITE; PS00072; ACYL_COA_DH_1; FALSE_NEG.
+DR PROSITE; PS00073; ACYL_COA_DH_2; 1.
+KW Hypothetical protein; Oxidoreductase; Flavoprotein; FAD; Mitochondrion;
+KW Transit peptide.
+FT TRANSIT 1 ? MITOCHONDRION (POTENTIAL)..
+FT CHAIN ? 409 PROBABLE GLUTARYL-COA DEHYDROGENASE..
+FT ACT_SITE 388 388 BASE (POTENTIAL)..
+SQ SEQUENCE 409 AA; 44965 MW; 4D06241FB6768069 CRC64;
+ MLTRGFTSIG KIASRGLSST FYQDAFQLSD QLTEDERSLM LSAREYCQER LLPRVTEAYR
+ TEKFDPSLIP EMGSMGLLGA PYQGYGCAGT STVGYGLIAR EVERVDSGYR STMSVQTSLV
+ IGPIYNYGSE DQKQKYIPDL ASGKKIGCFG LTEPNHGSNP GGMETKATWD ETTKTYKLNG
+ SKTWISNSPV SDVMVVWARS ARHNNKIKGF ILERGMKGLT TPKIEGKLSL RASITGQIAM
+ DDVPVPEENL LPNAEGLQGP FGCLNNARLG IAWGALGAAE ECFHLARQYT LDRQQFGRPL
+ AQNQLMQLKM ADMLTEISLG LQGCLRVSRL KDEGKVQSEQ ISIIKRNSCG KALEVARKAR
+ DMLGGNGIVD EYHIMRHMVN LETVNTYEGT HDVHALILGR AITGLNGFC
+//
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