Commit e995fe18 authored by Charles Plessy's avatar Charles Plessy

Split bioperl-run, install scripts, and enable network tests locally.

parent 5aa19405
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).
......@@ -14,6 +14,13 @@ bioperl-run (1.6.9-1) UNRELEASED; urgency=low
- 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/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,
-- Charles Plessy <> Fri, 17 Jun 2011 09:05:14 +0900
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 @@ Homepage:
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.
--- 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');
#!/usr/bin/make -f
NETWORK = --network
dh $@
dh $@ --with quilt
dh_auto_configure -- --install_scripts $(NETWORK)
PATH=$$PATH:/usr/lib/emboss dh_auto_test
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