Author: tbooth-guest Date: 2011-04-14 11:47:13 +0000 (Thu, 14 Apr 2011) New Revision: 6555
Added: trunk/packages/microbiomeutil/trunk/debian/patches/find_relocated_resources.patch trunk/packages/microbiomeutil/trunk/debian/patches/fix_perl_interpreter.patch Modified: trunk/packages/microbiomeutil/trunk/debian/README.Debian trunk/packages/microbiomeutil/trunk/debian/changelog trunk/packages/microbiomeutil/trunk/debian/control trunk/packages/microbiomeutil/trunk/debian/copyright trunk/packages/microbiomeutil/trunk/debian/patches/series trunk/packages/microbiomeutil/trunk/debian/rules Log: I reckon I'm 90% there with this. The package now splits into separate tools and puts things into sane (to my mind) locations. The main thing is I now have a chimeraslayer package to go with qiime, so I'm going back to that next. Modified: trunk/packages/microbiomeutil/trunk/debian/README.Debian =================================================================== --- trunk/packages/microbiomeutil/trunk/debian/README.Debian 2011-04-14 09:04:54 UTC (rev 6554) +++ trunk/packages/microbiomeutil/trunk/debian/README.Debian 2011-04-14 11:47:13 UTC (rev 6555) @@ -5,3 +5,8 @@ Volunteer maintainers please step forward. -- Steffen Moeller <[email protected]> Thu, 02 Dec 2010 09:39:26 +0100 + +Taken on in March 2011 by Tim Booth <[email protected]>. Split into 4 packages. +For info on this software please see this publication: + +http://genome.cshlp.org/content/21/3/494.abstract Modified: trunk/packages/microbiomeutil/trunk/debian/changelog =================================================================== --- trunk/packages/microbiomeutil/trunk/debian/changelog 2011-04-14 09:04:54 UTC (rev 6554) +++ trunk/packages/microbiomeutil/trunk/debian/changelog 2011-04-14 11:47:13 UTC (rev 6555) @@ -1,7 +1,13 @@ -microbiomeutil (20101212-1) unstable; urgency=low +microbiomeutil (20101212-1ubuntu1) lucid; urgency=low - * New upstream release. + * Split package into 4 binary packages. + -- Tim Booth <[email protected]> Mon, 11 Apr 2011 17:04:36 +0100 + +microbiomeutil (2010-11-1) unstable; urgency=low + + * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP> + -- Steffen Moeller <[email protected]> Wed, 30 Mar 2011 00:23:15 +0200 microbiomeutil (2010-11-02-1) UNRELEASED; urgency=low Modified: trunk/packages/microbiomeutil/trunk/debian/control =================================================================== --- trunk/packages/microbiomeutil/trunk/debian/control 2011-04-14 09:04:54 UTC (rev 6554) +++ trunk/packages/microbiomeutil/trunk/debian/control 2011-04-14 11:47:13 UTC (rev 6555) @@ -3,17 +3,16 @@ Priority: extra Maintainer: Debian Med Packaging Team <[email protected]> DM-Upload-Allowed: yes -Uploaders: Steffen Moeller <[email protected]> -Build-Depends: debhelper (>= 7.0.50~) +Uploaders: Steffen Moeller <[email protected]>, Tim Booth <[email protected]> +Build-Depends: debhelper (>= 7.0.50~), cdbfasta Standards-Version: 3.9.1 Homepage: http://microbiomeutil.sourceforge.net/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/microbiomeutil/trunk/?rev=0&sc=0 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/microbiomeutil/trunk/ Package: microbiomeutil -Provides: chimeraslayer, wigeon Architecture: all -Depends: ${misc:Depends} +Depends: ${misc:Depends}, chimeraslayer, nast-ier, wigeon Description: Microbiome Analysis Utilities The microbiomeutil package comes with the following utilities: * ChimeraSlayer: ChimeraSlayer for chimera detection. @@ -22,3 +21,26 @@ detection utility * RESOURCES: Reference 16S sequences and NAST-alignments that the tools above leverage. + +Package: chimeraslayer +Architecture: all +Depends: ${misc:Depends}, perl, microbiomeutil-data, cdbfasta +Description: Chimera detection + Part of the microbiomeutil package + +Package: nast-ier +Architecture: any +Depends: ${misc:Depends}, ${shlibs:Depends}, perl, microbiomeutil-data, cdbfasta +Description: NAST-based alignment tool + Part of the microbiomeutil package + +Package: wigeon +Architecture: all +Depends: ${misc:Depends}, perl, microbiomeutil-data +Description: A reimplementation of the Pintail 16S anomaly detection utility + Part of the microbiomeutil package + +Package: microbiomeutil-data +Architecture: all +Depends: ${misc:Depends} +Description: Reference 16S sequences and NAST-alignments used by microbiomeutil tools Modified: trunk/packages/microbiomeutil/trunk/debian/copyright =================================================================== --- trunk/packages/microbiomeutil/trunk/debian/copyright 2011-04-14 09:04:54 UTC (rev 6554) +++ trunk/packages/microbiomeutil/trunk/debian/copyright 2011-04-14 11:47:13 UTC (rev 6555) @@ -1,6 +1,7 @@ This work was packaged for Debian by: Steffen Moeller <[email protected]> on Thu, 02 Dec 2010 09:39:26 +0100 + Tim Booth <[email protected]> April 2011 It was downloaded from: @@ -8,15 +9,15 @@ Upstream Authors: - Brian Haas <[email protected]> + Brian J. Haas <[email protected]> Copyright: - Copyright (C) 2009-2011 Broad Institute (http://www.broadinstitute.org) + Copyright (C) 2010 The Broad Institute <http://www.broadinstitute.org> License: - Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: + See LICENSE files for each package. * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. @@ -48,3 +49,4 @@ and is licensed under the GPL version 3, see "/usr/share/common-licenses/GPL-3". + Added: trunk/packages/microbiomeutil/trunk/debian/patches/find_relocated_resources.patch =================================================================== --- trunk/packages/microbiomeutil/trunk/debian/patches/find_relocated_resources.patch (rev 0) +++ trunk/packages/microbiomeutil/trunk/debian/patches/find_relocated_resources.patch 2011-04-14 11:47:13 UTC (rev 6555) @@ -0,0 +1,50 @@ +--- a/ChimeraSlayer/ChimeraSlayer.pl ++++ b/ChimeraSlayer/ChimeraSlayer.pl +@@ -11,8 +11,8 @@ + use CdbTools; + use File::Basename; + +-my $db_NAST = "$FindBin::Bin/../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta"; +-my $db_FASTA = "$FindBin::Bin/../RESOURCES/rRNA16S.gold.fasta"; ++my $db_NAST = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta"; ++my $db_FASTA = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta"; + + + my $usage = <<_EOUSAGE_; +--- a/ChimeraSlayer/util/CS_add_taxonomy.pl ++++ b/ChimeraSlayer/util/CS_add_taxonomy.pl +@@ -13,7 +13,7 @@ + my %acc_to_taxonomy; + + { +- my $fasta_reader = new Fasta_reader("$FindBin::Bin/../../RESOURCES/rRNA16S.gold.fasta"); ++ my $fasta_reader = new Fasta_reader("/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta"); + while (my $seq_obj = $fasta_reader->next()) { + my $acc = $seq_obj->get_accession; + +--- a/NAST-iEr/run_NAST-iEr.pl ++++ b/NAST-iEr/run_NAST-iEr.pl +@@ -12,8 +12,8 @@ + use Nuc_translator; + + +-my $db_FASTA = "$FindBin::Bin/..//RESOURCES/rRNA16S.gold.fasta"; +-my $db_NAST = "$FindBin::Bin/../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta"; ++my $db_FASTA = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta"; ++my $db_NAST = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta"; + + + my $usage = <<_EOUSAGE_; +--- a/WigeoN/run_WigeoN.pl ++++ b/WigeoN/run_WigeoN.pl +@@ -12,8 +12,8 @@ + use CdbTools; + + +-my $refDB = "$FindBin::Bin/../RESOURCES/rRNA16S.gold.fasta"; +-my $refNAST = "$FindBin::Bin/../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta"; ++my $refDB = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta"; ++my $refNAST = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta"; + + my $usage = <<__EOUSAGE__; + Added: trunk/packages/microbiomeutil/trunk/debian/patches/fix_perl_interpreter.patch =================================================================== --- trunk/packages/microbiomeutil/trunk/debian/patches/fix_perl_interpreter.patch (rev 0) +++ trunk/packages/microbiomeutil/trunk/debian/patches/fix_perl_interpreter.patch 2011-04-14 11:47:13 UTC (rev 6555) @@ -0,0 +1,24 @@ +--- a/NAST-iEr/PerlLib/Fasta_reader.pm ++++ b/NAST-iEr/PerlLib/Fasta_reader.pm +@@ -1,5 +1,3 @@ +-#!/usr/local/bin/perl -w +- + # lightweight fasta reader capabilities: + package Fasta_reader; + +--- a/ChimeraSlayer/PerlLib/Fasta_reader.pm ++++ b/ChimeraSlayer/PerlLib/Fasta_reader.pm +@@ -1,5 +1,3 @@ +-#!/usr/local/bin/perl -w +- + # lightweight fasta reader capabilities: + package Fasta_reader; + +--- a/WigeoN/PerlLib/Fasta_reader.pm ++++ b/WigeoN/PerlLib/Fasta_reader.pm +@@ -1,5 +1,3 @@ +-#!/usr/local/bin/perl -w +- + # lightweight fasta reader capabilities: + package Fasta_reader; + Modified: trunk/packages/microbiomeutil/trunk/debian/patches/series =================================================================== --- trunk/packages/microbiomeutil/trunk/debian/patches/series 2011-04-14 09:04:54 UTC (rev 6554) +++ trunk/packages/microbiomeutil/trunk/debian/patches/series 2011-04-14 11:47:13 UTC (rev 6555) @@ -1 +1,3 @@ -#Makefile_make_no_NAST.patch +fix_perl_interpreter.patch +find_relocated_resources.patch +Makefile_make_no_NAST.patch Modified: trunk/packages/microbiomeutil/trunk/debian/rules =================================================================== --- trunk/packages/microbiomeutil/trunk/debian/rules 2011-04-14 09:04:54 UTC (rev 6554) +++ trunk/packages/microbiomeutil/trunk/debian/rules 2011-04-14 11:47:13 UTC (rev 6555) @@ -11,3 +11,32 @@ %: dh $@ + +#Kill the tests just now - they take too long. +override_dh_auto_test : + true + +#OK, I can't fathom all the auto-install stuff, and I'm not sure +#it will work properly for this package in any case. Do it manually. +#Note that NAST-iEr comes with a binary but users are expected to run it via the Perl wrapper. +export DH_INSTALL=dh_install -XMakefile -Xsample_data -XLICENSE -XNAST-iEr.c +override_dh_install : + dh_installdirs -A /usr/bin + $(DH_INSTALL) -pchimeraslayer ChimeraSlayer /usr/share + ln -s /usr/share/ChimeraSlayer/ChimeraSlayer.pl debian/chimeraslayer/usr/bin/chimeraslayer + dh_install -pchimeraslayer ChimeraSlayer/LICENSE /usr/share/doc/chimeraslayer + $(DH_INSTALL) -pwigeon WigeoN /usr/share + ln -s /usr/share/WigeoN/run_WigeoN.pl debian/wigeon/usr/bin/wigeon + ln -s /usr/share/WigeoN/run_CM_to_WigeoN.pl debian/wigeon/usr/bin/cm_to_wigeon + dh_install -pwigeon WigeoN/LICENSE /usr/share/doc/wigeon + $(DH_INSTALL) -pnast-ier NAST-iEr /usr/share + ln -s /usr/share/NAST-iEr/run_NAST-iEr.pl debian/nast-ier/usr/bin/nast-ier + dh_install -pnast-ier NAST-iEr/LICENSE /usr/share/doc/nast-ier + $(DH_INSTALL) -pmicrobiomeutil-data RESOURCES /usr/share/microbiomeutil-data + $(DH_INSTALL) -pmicrobiomeutil-data ChimeraSlayer/sample_data/* /usr/share/microbiomeutil-data/ChimeraSlayer + $(DH_INSTALL) -pmicrobiomeutil-data WigeoN/sample_data/* /usr/share/microbiomeutil-data/ChimeraSlayer + $(DH_INSTALL) -pmicrobiomeutil-data NAST-iEr/sample_data/* /usr/share/microbiomeutil-data/ChimeraSlayer + +override_dh_fixperms : + dh_fixperms + find debian -type f -name '*.pm' -print0 | xargs -0r chmod a-x _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
