[med-svn] r6555 - in trunk/packages/microbiomeutil/trunk/debian: . patches
Timothy Booth
tbooth-guest at alioth.debian.org
Thu Apr 14 11:47:14 UTC 2011
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 <moeller at debian.org> Thu, 02 Dec 2010 09:39:26 +0100
+
+Taken on in March 2011 by Tim Booth <tbooth at ceh.ac.uk>. 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 <tbooth at ceh.ac.uk> 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 <moeller at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
-Uploaders: Steffen Moeller <moeller at debian.org>
-Build-Depends: debhelper (>= 7.0.50~)
+Uploaders: Steffen Moeller <moeller at debian.org>, Tim Booth <tbooth at ceh.ac.uk>
+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 <moeller at debian.org> on Thu, 02 Dec 2010 09:39:26 +0100
+ Tim Booth <tbooth at ceh.ac.uk> April 2011
It was downloaded from:
@@ -8,15 +9,15 @@
Upstream Authors:
- Brian Haas <bhaas at broadinstitute.org>
+ Brian J. Haas <bhaas at broadinstitute.org>
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
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