Author: tbooth-guest Date: 2013-06-03 15:45:49 +0000 (Mon, 03 Jun 2013) New Revision: 13818
Added: trunk/packages/microbiomeutil/trunk/debian/patches/find_relocated_libraries.patch Modified: trunk/packages/microbiomeutil/trunk/debian/changelog trunk/packages/microbiomeutil/trunk/debian/control trunk/packages/microbiomeutil/trunk/debian/patches/fix_perl_interpreter.patch trunk/packages/microbiomeutil/trunk/debian/patches/series trunk/packages/microbiomeutil/trunk/debian/rules Log: My latest changes and better descriptions as requested. Modified: trunk/packages/microbiomeutil/trunk/debian/changelog =================================================================== --- trunk/packages/microbiomeutil/trunk/debian/changelog 2013-06-03 14:57:06 UTC (rev 13817) +++ trunk/packages/microbiomeutil/trunk/debian/changelog 2013-06-03 15:45:49 UTC (rev 13818) @@ -1,3 +1,13 @@ +microbiomeutil (20101212-1ubuntu6) lucid; urgency=low + + * Another patch needed to Perl code due to inappropriate use of + FindBin + * Move to /usr/lib rather than /usr/share as per Lintian warnings. + * Set --with quilt on dh. (Possibly not needed now?) + * Added better descriptions in debian/control + + -- Tim Booth <[email protected]> Mon, 03 Jun 2013 16:44:30 +0100 + microbiomeutil (20101212-1) UNRELEASED; urgency=low * debian/copyright: DEP5 copyright Modified: trunk/packages/microbiomeutil/trunk/debian/control =================================================================== --- trunk/packages/microbiomeutil/trunk/debian/control 2013-06-03 14:57:06 UTC (rev 13817) +++ trunk/packages/microbiomeutil/trunk/debian/control 2013-06-03 15:45:49 UTC (rev 13818) @@ -4,7 +4,7 @@ Maintainer: Debian Med Packaging Team <[email protected]> DM-Upload-Allowed: yes Uploaders: Steffen Moeller <[email protected]>, Tim Booth <[email protected]> -Build-Depends: debhelper (>= 7.0.50~), cdbfasta +Build-Depends: debhelper (>= 7.0.50~), cdbfasta, quilt (>= 0.46-7~) Standards-Version: 3.9.1 Homepage: http://microbiomeutil.sourceforge.net/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/microbiomeutil/trunk/ @@ -25,22 +25,31 @@ Package: chimeraslayer Architecture: all Depends: ${misc:Depends}, perl, microbiomeutil-data, cdbfasta -Description: Chimera detection - Part of the microbiomeutil package +Description: detects likely chimeras in PCR amplified DNA + ChimeraSlayer is from the microbiomeutil package. + . + http://microbiomeutil.sourceforge.net/#A_CS Package: nast-ier Architecture: any Depends: ${misc:Depends}, ${shlibs:Depends}, perl, microbiomeutil-data, cdbfasta -Description: NAST-based alignment tool - Part of the microbiomeutil package +Description: NAST-based DNA alignment tool + NAST-iEr is from the microbiomeutil package. + . + http://microbiomeutil.sourceforge.net/#A_NASTiEr 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 +Description: reimplementation of the Pintail 16S DNA anomaly detection utility + WigeoN is from the microbiomeutil package + . + http://microbiomeutil.sourceforge.net/#A_WigeoN Package: microbiomeutil-data Architecture: all Depends: ${misc:Depends} Description: Reference 16S sequences and NAST-alignments used by microbiomeutil tools + Reference data for tools in the microbiomeutil package. + . + http://microbiomeutil.sourceforge.net Added: trunk/packages/microbiomeutil/trunk/debian/patches/find_relocated_libraries.patch =================================================================== --- trunk/packages/microbiomeutil/trunk/debian/patches/find_relocated_libraries.patch (rev 0) +++ trunk/packages/microbiomeutil/trunk/debian/patches/find_relocated_libraries.patch 2013-06-03 15:45:49 UTC (rev 13818) @@ -0,0 +1,71 @@ +# Due to liberal use of FindBin, ChimeraSlayer can't be run from a symlink. +# So I'm hard-coding the location to get around this. +# Patch added by Tim Booth, see changelog +--- a/ChimeraSlayer/ChimeraSlayer.pl ++++ b/ChimeraSlayer/ChimeraSlayer.pl +@@ -4,7 +4,9 @@ + use warnings; + + use Getopt::Long qw(:config no_ignore_case bundling); +-use FindBin; ++#use FindBin; ++#Hack needed because FindBin is braindead. ++BEGIN{ $FindBin::Bin = "/usr/lib/ChimeraSlayer" }; + + use lib ("$FindBin::Bin/PerlLib"); + use Fasta_reader; +--- a/NAST-iEr/run_NAST-iEr.pl ++++ b/NAST-iEr/run_NAST-iEr.pl +@@ -5,7 +5,9 @@ + + use Getopt::Long; + +-use FindBin; ++#use FindBin; ++##Hack needed because FindBin is braindead. ++BEGIN{ $FindBin::Bin = "/usr/lib/NAST-iEr" }; + use lib ("$FindBin::Bin/PerlLib"); + use Fasta_reader; + use CdbTools; +--- a/WigeoN/WigeoN.pl ++++ b/WigeoN/WigeoN.pl +@@ -5,7 +5,9 @@ + + use Carp; + use Getopt::Long qw(:config no_ignore_case bundling); +-use FindBin; ++#use FindBin; ++#Hack needed because FindBin is braindead. ++BEGIN{ $FindBin::Bin = "/usr/lib/WigeoN" }; + use POSIX; + + use lib ("$FindBin::Bin/PerlLib"); +--- a/WigeoN/run_CM_to_WigeoN.pl ++++ b/WigeoN/run_CM_to_WigeoN.pl +@@ -4,9 +4,11 @@ + use warnings; + + use Getopt::Long qw(:config no_ignore_case bundling); +-use FindBin; ++#use FindBin; ++#Hack needed because FindBin is braindead. ++BEGIN{ $FindBin::Bin = "/usr/lib/WigeoN" }; + +-use lib ("$FindBin::Bin/../PerlLib"); ++use lib ("$FindBin::Bin/PerlLib"); + use Fasta_reader; + use CdbTools; + +--- a/WigeoN/run_WigeoN.pl ++++ b/WigeoN/run_WigeoN.pl +@@ -5,7 +5,9 @@ + + use Carp; + use Getopt::Long qw(:config no_ignore_case bundling); +-use FindBin; ++#use FindBin; ++#Hack needed because FindBin is braindead. ++#BEGIN{ $FindBin::Bin = "/usr/lib/WigeoN" }; + + use lib ("$FindBin::Bin/PerlLib"); + use Fasta_reader; Modified: trunk/packages/microbiomeutil/trunk/debian/patches/fix_perl_interpreter.patch =================================================================== --- trunk/packages/microbiomeutil/trunk/debian/patches/fix_perl_interpreter.patch 2013-06-03 14:57:06 UTC (rev 13817) +++ trunk/packages/microbiomeutil/trunk/debian/patches/fix_perl_interpreter.patch 2013-06-03 15:45:49 UTC (rev 13818) @@ -22,3 +22,11 @@ # lightweight fasta reader capabilities: package Fasta_reader; +--- a/RESOURCES/genus_counter.pl ++++ b/RESOURCES/genus_counter.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + use strict; + use warnings; Modified: trunk/packages/microbiomeutil/trunk/debian/patches/series =================================================================== --- trunk/packages/microbiomeutil/trunk/debian/patches/series 2013-06-03 14:57:06 UTC (rev 13817) +++ trunk/packages/microbiomeutil/trunk/debian/patches/series 2013-06-03 15:45:49 UTC (rev 13818) @@ -1,3 +1,3 @@ fix_perl_interpreter.patch find_relocated_resources.patch -Makefile_make_no_NAST.patch +find_relocated_libraries.patch Modified: trunk/packages/microbiomeutil/trunk/debian/rules =================================================================== --- trunk/packages/microbiomeutil/trunk/debian/rules 2013-06-03 14:57:06 UTC (rev 13817) +++ trunk/packages/microbiomeutil/trunk/debian/rules 2013-06-03 15:45:49 UTC (rev 13818) @@ -1,36 +1,33 @@ #!/usr/bin/make -f # -*- makefile -*- -# Sample debian/rules that uses debhelper. -# This file was originally written by Joey Hess and Craig Small. -# As a special exception, when this file is copied by dh-make into a -# dh-make output file, you may use that output file without restriction. -# This special exception was added by Craig Small in version 0.37 of dh-make. # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 %: - dh $@ + dh $@ --with quilt #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. +#it will work properly for this package in any case. Doing 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 +export DH_LINK=dh_link 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 + #Included -v to debug remote build + dh_installdirs -v -A /usr/bin + $(DH_INSTALL) -pchimeraslayer ChimeraSlayer /usr/lib + $(DH_LINK) -pchimeraslayer /usr/lib/ChimeraSlayer/ChimeraSlayer.pl /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 /usr/lib + $(DH_LINK) -pwigeon /usr/lib/WigeoN/run_WigeoN.pl /usr/bin/wigeon + $(DH_LINK) -pwigeon /usr/lib/WigeoN/run_CM_to_WigeoN.pl /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 /usr/lib + $(DH_LINK) -pnast-ier /usr/lib/NAST-iEr/run_NAST-iEr.pl /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 @@ -40,3 +37,4 @@ override_dh_fixperms : dh_fixperms find debian -type f -name '*.pm' -print0 | xargs -0r chmod a-x + find debian -type f -name 'genus_counter.pl' -print0 | xargs -0r chmod a+x _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
