Author: moeller Date: 2011-07-14 16:08:04 +0000 (Thu, 14 Jul 2011) New Revision: 7281
Added: trunk/packages/chado/trunk/debian/ trunk/packages/chado/trunk/debian/changelog trunk/packages/chado/trunk/debian/compat trunk/packages/chado/trunk/debian/control trunk/packages/chado/trunk/debian/copyright trunk/packages/chado/trunk/debian/libchado-perl.dirs trunk/packages/chado/trunk/debian/libchado-perl.docs trunk/packages/chado/trunk/debian/libchado-perl.examples trunk/packages/chado/trunk/debian/patches/ trunk/packages/chado/trunk/debian/patches/error_message.patch trunk/packages/chado/trunk/debian/patches/no_tests.patch trunk/packages/chado/trunk/debian/patches/series trunk/packages/chado/trunk/debian/rules trunk/packages/chado/trunk/debian/watch Log: Details of Chado packaging. Added: trunk/packages/chado/trunk/debian/changelog =================================================================== --- trunk/packages/chado/trunk/debian/changelog (rev 0) +++ trunk/packages/chado/trunk/debian/changelog 2011-07-14 16:08:04 UTC (rev 7281) @@ -0,0 +1,5 @@ +libchado-perl (1.12-1) unstable; urgency=low + + * Initial Release. + + -- Steffen Moeller <[email protected]> Thu, 14 Jul 2011 12:44:56 +0200 Added: trunk/packages/chado/trunk/debian/compat =================================================================== --- trunk/packages/chado/trunk/debian/compat (rev 0) +++ trunk/packages/chado/trunk/debian/compat 2011-07-14 16:08:04 UTC (rev 7281) @@ -0,0 +1 @@ +8 Added: trunk/packages/chado/trunk/debian/control =================================================================== --- trunk/packages/chado/trunk/debian/control (rev 0) +++ trunk/packages/chado/trunk/debian/control 2011-07-14 16:08:04 UTC (rev 7281) @@ -0,0 +1,22 @@ +Source: libchado-perl +Section: perl +Priority: optional +Maintainer: Steffen Moeller <[email protected]> +Build-Depends: debhelper (>= 8) +Build-Depends-Indep: perl, libtemplate-perl, libclass-dbi-pg-perl, libclass-dbi-pager-perl, libxml-libxslt-perl +Standards-Version: 3.9.2 +Homepage: http://search.cpan.org/dist/chado/ + +Package: libchado-perl +Architecture: all +Depends: ${misc:Depends}, ${perl:Depends} +Description: database schema and tools for genomic data + Chado is a relational database schema that underlies many GMOD + installations. It is capable of representing many of the general + classes of data frequently encountered in modern biology such as + sequence, sequence comparisons, phenotypes, genotypes, ontologies, + publications, and phylogeny. It has been designed to handle complex + representations of biological knowledge and should be considered one + of the most sophisticated relational schemas currently available in + molecular biology. The price of this capability is that the new user + must spend some time becoming familiar with its fundamentals. Added: trunk/packages/chado/trunk/debian/copyright =================================================================== --- trunk/packages/chado/trunk/debian/copyright (rev 0) +++ trunk/packages/chado/trunk/debian/copyright 2011-07-14 16:08:04 UTC (rev 7281) @@ -0,0 +1,231 @@ +Format-Specification: http://svn.debian.org/wsvn/dep/web/deps/dep5.mdwn?op=file&rev=135 +Maintainer: Scott Cain <[email protected]> +Source: http://gmod.org/wiki/Chado_-_Getting_Started +Name: chado + +Files: * +Copyright: Scott Cain <[email protected]> +License: Artistic-2.0 + +Files: debian/* +Copyright: 2011, Steffen Moeller <[email protected]> +License: Artistic-2.0 or Artistic or GPL-1+ + +License: Artistic-2.0 + The Artistic License 2.0 + . + Copyright (c) 2000-2006, The Perl Foundation. + . + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + . + Preamble + . + This license establishes the terms under which a given free software + Package may be copied, modified, distributed, and/or redistributed. + The intent is that the Copyright Holder maintains some artistic + control over the development of that Package while still keeping the + Package available as open source and free software. + . + You are always permitted to make arrangements wholly outside of this + license directly with the Copyright Holder of a given Package. If the + terms of this license do not permit the full use that you propose to + make of the Package, you should contact the Copyright Holder and seek + a different licensing arrangement. + . + Definitions + . + "Copyright Holder" means the individual(s) or organization(s) + named in the copyright notice for the entire Package. + . + "Contributor" means any party that has contributed code or other + material to the Package, in accordance with the Copyright Holder's + procedures. + . + "You" and "your" means any person who would like to copy, + distribute, or modify the Package. + . + "Package" means the collection of files distributed by the + Copyright Holder, and derivatives of that collection and/or of + those files. 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Added: trunk/packages/chado/trunk/debian/libchado-perl.dirs =================================================================== --- trunk/packages/chado/trunk/debian/libchado-perl.dirs (rev 0) +++ trunk/packages/chado/trunk/debian/libchado-perl.dirs 2011-07-14 16:08:04 UTC (rev 7281) @@ -0,0 +1 @@ +usr/share/gmod/chado Added: trunk/packages/chado/trunk/debian/libchado-perl.docs =================================================================== --- trunk/packages/chado/trunk/debian/libchado-perl.docs (rev 0) +++ trunk/packages/chado/trunk/debian/libchado-perl.docs 2011-07-14 16:08:04 UTC (rev 7281) @@ -0,0 +1,13 @@ +README.Apollo +TODO +README +modules/phylogeny/examples/README +modules/sequence/bdgp/README +modules/sequence/apollo-bridge/sample_db/README +load/etc/README +stag-templates/README +chaos-xml/README +chaos-xml/xsl/README +chado-xml/README +chado-xml/xsl/README +soi/README Added: trunk/packages/chado/trunk/debian/libchado-perl.examples =================================================================== --- trunk/packages/chado/trunk/debian/libchado-perl.examples (rev 0) +++ trunk/packages/chado/trunk/debian/libchado-perl.examples 2011-07-14 16:08:04 UTC (rev 7281) @@ -0,0 +1,4 @@ +modules/phylogeny/examples +modules/organism/examples +chado-xml/examples +doc/examples Added: trunk/packages/chado/trunk/debian/patches/error_message.patch =================================================================== --- trunk/packages/chado/trunk/debian/patches/error_message.patch (rev 0) +++ trunk/packages/chado/trunk/debian/patches/error_message.patch 2011-07-14 16:08:04 UTC (rev 7281) @@ -0,0 +1,19 @@ +Index: chado-1.11/install_util/conf_install.pl +=================================================================== +--- chado-1.11.orig/install_util/conf_install.pl 2011-07-14 14:53:38.768356998 +0200 ++++ chado-1.11/install_util/conf_install.pl 2011-07-14 14:54:20.884565859 +0200 +@@ -47,12 +47,12 @@ + my $defaultconf = "$confdir/default.conf"; + my $dbconf = "$confdir/$confitems{DBNAME}.conf"; + +-open GMODCONF, ">$gmodconf" or die "unable to open $gmodconf: $!"; ++open GMODCONF, ">$gmodconf" or die "unable to open $gmodconf for writing: $!"; + print GMODCONF "CONF=$gmod_root/conf\n"; + print GMODCONF "TMP=$gmod_root/tmp\n"; + close GMODCONF; + +-open DBCONF, ">$dbconf" or die "unable to open $dbconf: $!"; ++open DBCONF, ">$dbconf" or die "unable to open $dbconf for writing: $!"; + foreach my $key (keys %confitems) { + print DBCONF "$key=$confitems{$key}\n"; + } Added: trunk/packages/chado/trunk/debian/patches/no_tests.patch =================================================================== --- trunk/packages/chado/trunk/debian/patches/no_tests.patch (rev 0) +++ trunk/packages/chado/trunk/debian/patches/no_tests.patch 2011-07-14 16:08:04 UTC (rev 7281) @@ -0,0 +1,18 @@ +Index: chado-1.11/t/01_okay.t +=================================================================== +--- chado-1.11.orig/t/01_okay.t 2011-07-14 15:00:29.786395125 +0200 ++++ chado-1.11/t/01_okay.t 2011-07-14 15:14:09.578460264 +0200 +@@ -2,9 +2,11 @@ + use strict; + # change 'tests => 1' to 'tests => last_test_to_print'; + +-use Test::More tests => 1; ++#use Test::More 0.96; ++use Test::More skip_all => "Just not testing."; + use lib 'lib'; +-BEGIN { use_ok('Bio::Chado::LoadDBI') }; ++ ++ok(1); + + ######################### + Added: trunk/packages/chado/trunk/debian/patches/series =================================================================== --- trunk/packages/chado/trunk/debian/patches/series (rev 0) +++ trunk/packages/chado/trunk/debian/patches/series 2011-07-14 16:08:04 UTC (rev 7281) @@ -0,0 +1,3 @@ +error_message.patch +no_tests.patch +no_chaos.patch Added: trunk/packages/chado/trunk/debian/rules =================================================================== --- trunk/packages/chado/trunk/debian/rules (rev 0) +++ trunk/packages/chado/trunk/debian/rules 2011-07-14 16:08:04 UTC (rev 7281) @@ -0,0 +1,23 @@ +#!/usr/bin/make -f + +#export GMOD_ROOT=/usr/share/gmod/chado +export GMOD_ROOT=$(CURDIR)/debian/libchado-perl/usr/share/gmod/chado +export CHAOS_HOME=$(CURDIR)/debian/libchado-perl/usr/share/gmod/chaos +export CHADO_DB_NAME=gmod-chado +export PREFIX=/usr + +#$(CURDIR)/debian/libchado-perl/usr/share/gmod/chado/conf: +# mkdir -p $(CURDIR)/debian/libchado-perl/usr/share/gmod/chado/conf +# touch $(CURDIR)/debian/libchado-perl/usr/share/gmod/chado/conf/gmod.conf +# touch $(CURDIR)/debian/libchado-perl/usr/share/gmod/chado/conf/default.conf +# +#%: $(CURDIR)/debian/libchado-perl/usr/share/gmod/chado/conf + +%: + dh $@ --buildsystem=perl_makemaker + +override_dh_auto_configure: + perl Makefile.PL INSTALL_BASE=/usr + +override_dh_auto_test: + echo "Not testing." Property changes on: trunk/packages/chado/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/chado/trunk/debian/watch =================================================================== --- trunk/packages/chado/trunk/debian/watch (rev 0) +++ trunk/packages/chado/trunk/debian/watch 2011-07-14 16:08:04 UTC (rev 7281) @@ -0,0 +1,2 @@ +version=3 +http://search.cpan.org/dist/chado/ .*/chado-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$ _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
