[med-svn] r7072 - in trunk/packages/bioperl-run/trunk/debian: . patches
Charles Plessy
plessy at alioth.debian.org
Fri Jun 17 09:31:17 UTC 2011
Author: plessy
Date: 2011-06-17 09:31:16 +0000 (Fri, 17 Jun 2011)
New Revision: 7072
Added:
trunk/packages/bioperl-run/trunk/debian/README.test
trunk/packages/bioperl-run/trunk/debian/bioperl-run.install
trunk/packages/bioperl-run/trunk/debian/libbio-perl-run-perl.install
trunk/packages/bioperl-run/trunk/debian/patches/
trunk/packages/bioperl-run/trunk/debian/patches/install-scripts.patch
trunk/packages/bioperl-run/trunk/debian/patches/series
Modified:
trunk/packages/bioperl-run/trunk/debian/changelog
trunk/packages/bioperl-run/trunk/debian/control
trunk/packages/bioperl-run/trunk/debian/rules
Log:
Split bioperl-run, install scripts, and enable network tests locally.
Added: trunk/packages/bioperl-run/trunk/debian/README.test
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/README.test (rev 0)
+++ trunk/packages/bioperl-run/trunk/debian/README.test 2011-06-17 09:31:16 UTC (rev 7072)
@@ -0,0 +1,5 @@
+Some upstream regression tests require access to Internet ressources, so they
+are disabled by default as network connectivity is not guaranteed in the Debian
+build daemons. But it is very recommended to run them locally before uploading
+this package. To do this, set the DEB_MAINTAINER_MODE environment variable
+(see debian/rules).
Added: trunk/packages/bioperl-run/trunk/debian/bioperl-run.install
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/bioperl-run.install (rev 0)
+++ trunk/packages/bioperl-run/trunk/debian/bioperl-run.install 2011-06-17 09:31:16 UTC (rev 7072)
@@ -0,0 +1,2 @@
+usr/bin
+usr/share/man/man1
Modified: trunk/packages/bioperl-run/trunk/debian/changelog
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/changelog 2011-06-17 08:54:23 UTC (rev 7071)
+++ trunk/packages/bioperl-run/trunk/debian/changelog 2011-06-17 09:31:16 UTC (rev 7072)
@@ -14,6 +14,13 @@
- Removed useless ‘svn’ in the Vcs-Svn URL.
* Point debian/watch to CPAN.
* Tiny style with Debhelper 8 (debian/rules, debian/compat, debian/control).
+ * Split scripts in bioperl-run and modules in libbio-perl-run-perl.
+ (debian/rules, debian/control, debian/bioperl-run.install,
+ debian/libbio-perl-run-perl.install)
+ * debian/patches/install-scripts.patch for Build.PL option --install_scripts.
+ (debian/rules, debian/patches/series, debian/control)
+ * Trigger network tests with DEB_MAINTAINER_MODE (debian/rules,
+ debian/README.test).
-- Charles Plessy <plessy at debian.org> Fri, 17 Jun 2011 09:05:14 +0900
Modified: trunk/packages/bioperl-run/trunk/debian/control
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/control 2011-06-17 08:54:23 UTC (rev 7071)
+++ trunk/packages/bioperl-run/trunk/debian/control 2011-06-17 09:31:16 UTC (rev 7072)
@@ -1,7 +1,7 @@
Source: bioperl-run
Section: science
Priority: optional
-Build-Depends: debhelper (>= 8), libmodule-build-perl
+Build-Depends: debhelper (>= 8), quilt, libmodule-build-perl
Build-Depends-Indep: perl, bioperl (>= 1.6.0), libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl,
libarray-compare-perl, libtree-dagnode-perl
# Here is a list of all the packages and prospective packages for which wrappers are provided.
@@ -21,16 +21,22 @@
Package: bioperl-run
Architecture: all
-Depends: ${misc:Depends}, ${perl:Depends}, bioperl (>= 1.6.0)
+Depends: ${misc:Depends}, ${perl:Depends}, bioperl (>= 1.6.0), libbio-perl-run-perl (= ${source:Version})
+Recommends: amap-align, blast2, clustalw, emboss, ensembl, hmmer, sim4, t-coffee, wise
+Suggests: coils, eponine, footprinter, genscan, pise, fingerprintscan, prscan, repeatmasker,
+ seg, signalp, tmhmm, tribe, paml, molphy, phylip, fasta, lagan, vista-align, blat
+Description: BioPerl wrappers: scripts
+ Contains scripts from the the BioPerl-Run package. This package will also install all
+ wrappable applications packaged in Debian. The ones that are not available or not Free are
+ "Suggested" by this package.
+
+Package: libbio-perl-run-perl
+Architecture: all
+Breaks: bioperl-run (<< 1.6.9)
+Replaces: bioperl-run (<< 1.6.9)
+Depends: ${misc:Depends}, ${perl:Depends}, libbio-perl-perl (>= 1.6.0)
Recommends: libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl, libwww-perl
-Suggests: coils, emboss, eponine, footprinter, wise, genscan, hmmer, pise,
- ensembl, fingerprintscan, prscan, repeatmasker, seg, signalp, tmhmm, tribe,
- paml, molphy, phylip, clustalw, sim4, t-coffee, blast2, fasta, lagan,
- vista-align, amap-align, blat
-Description: Wrapper modules for BioPerl
+Description: BioPerl wrappers: modules
Contains modules that provide a Perl interface to various
bioinformatics applications to allow them to be
used with common BioPerl objects.
- .
- Not all the wrappable applications are packaged in Debian. The ones
- that are are "Suggested" by this package.
Added: trunk/packages/bioperl-run/trunk/debian/libbio-perl-run-perl.install
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/libbio-perl-run-perl.install (rev 0)
+++ trunk/packages/bioperl-run/trunk/debian/libbio-perl-run-perl.install 2011-06-17 09:31:16 UTC (rev 7072)
@@ -0,0 +1,2 @@
+usr/share/perl5
+usr/share/man/man3
Added: trunk/packages/bioperl-run/trunk/debian/patches/install-scripts.patch
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/patches/install-scripts.patch (rev 0)
+++ trunk/packages/bioperl-run/trunk/debian/patches/install-scripts.patch 2011-06-17 09:31:16 UTC (rev 7072)
@@ -0,0 +1,21 @@
+--- a/Build.PL 2011-06-17 18:19:24.491792863 +0900
++++ b/Build.PL.install-scripts 2011-06-17 18:18:46.371792871 +0900
+@@ -27,7 +27,8 @@
+ },
+ get_options => {
+ accept => { },
+- network => { }
++ network => { },
++ install_scripts => { }
+ },
+ auto_features => {
+ Network => {
+@@ -42,7 +43,7 @@
+ my $accept = $build->args->{accept};
+
+ # Optionally have script files installed.
+-if ($accept ? 0 : $build->y_n("Install scripts? y/n", 'n')) {
++if ($build->args('install_scripts') or $accept ? 0 : $build->y_n("Install scripts? y/n", 'n')) {
+ my $files = $build->_find_file_by_type('PLS', 'scripts');
+
+ my $script_build = File::Spec->catdir($build->blib, 'script');
Added: trunk/packages/bioperl-run/trunk/debian/patches/series
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/patches/series (rev 0)
+++ trunk/packages/bioperl-run/trunk/debian/patches/series 2011-06-17 09:31:16 UTC (rev 7072)
@@ -0,0 +1 @@
+install-scripts.patch
Modified: trunk/packages/bioperl-run/trunk/debian/rules
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/rules 2011-06-17 08:54:23 UTC (rev 7071)
+++ trunk/packages/bioperl-run/trunk/debian/rules 2011-06-17 09:31:16 UTC (rev 7072)
@@ -1,6 +1,14 @@
#!/usr/bin/make -f
+
+ifneq (,$(DEB_MAINTAINER_MODE))
+NETWORK = --network
+endif
+
%:
- dh $@
+ dh $@ --with quilt
+override_dh_auto_configure:
+ dh_auto_configure -- --install_scripts $(NETWORK)
+
override_dh_auto_test:
PATH=$$PATH:/usr/lib/emboss dh_auto_test
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