[med-svn] r13818 - in trunk/packages/microbiomeutil/trunk/debian: . patches
Timothy Booth
tbooth-guest at alioth.debian.org
Mon Jun 3 15:45:49 UTC 2013
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 <tbooth at ceh.ac.uk> 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 <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Steffen Moeller <moeller at debian.org>, Tim Booth <tbooth at ceh.ac.uk>
-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
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