Author: osallou Date: 2012-03-19 08:54:49 +0000 (Mon, 19 Mar 2012) New Revision: 10023
Added: trunk/packages/gmod/chado/trunk/debian/patches/remove_pl_extension.patch Modified: trunk/packages/gmod/chado/trunk/debian/changelog trunk/packages/gmod/chado/trunk/debian/control trunk/packages/gmod/chado/trunk/debian/patches/series Log: add patch to call binary deps without perl extension Modified: trunk/packages/gmod/chado/trunk/debian/changelog =================================================================== --- trunk/packages/gmod/chado/trunk/debian/changelog 2012-03-19 08:53:48 UTC (rev 10022) +++ trunk/packages/gmod/chado/trunk/debian/changelog 2012-03-19 08:54:49 UTC (rev 10023) @@ -1,3 +1,10 @@ +libchado-perl (1.22-3) unstable; urgency=low + + * debian/patches/remove_pl_extension.patch: + - add patch to use libdbix-dbstag-perl binary without extension + + -- Olivier Sallou <[email protected]> Mon, 19 Mar 2012 09:26:00 +0100 + libchado-perl (1.22-2) unstable; urgency=low [Olivier Sallou] Modified: trunk/packages/gmod/chado/trunk/debian/control =================================================================== --- trunk/packages/gmod/chado/trunk/debian/control 2012-03-19 08:53:48 UTC (rev 10022) +++ trunk/packages/gmod/chado/trunk/debian/control 2012-03-19 08:54:49 UTC (rev 10023) @@ -2,7 +2,7 @@ Section: perl Priority: optional Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Scott Cain <[email protected]>, Steffen Moeller <[email protected]>, Olivier Sallou <[email protected]> +Uploaders: Scott Cain <[email protected]>, Steffen Moeller <[email protected]>, Olivier Sallou <[email protected]> DM-Upload-Allowed: yes Build-Depends: debhelper (>= 8) Build-Depends-Indep: perl, libclass-dbi-pg-perl, libxml-libxslt-perl, liblog-log4perl-perl, Added: trunk/packages/gmod/chado/trunk/debian/patches/remove_pl_extension.patch =================================================================== --- trunk/packages/gmod/chado/trunk/debian/patches/remove_pl_extension.patch (rev 0) +++ trunk/packages/gmod/chado/trunk/debian/patches/remove_pl_extension.patch 2012-03-19 08:54:49 UTC (rev 10023) @@ -0,0 +1,48 @@ +Subject: remove extension to call libdbix-dbstag-perl binaries +Description: libdbix-dbstag-perl binaries have perl extension removed, + current scripts must call those binaries without extension too +Author: Olivier Sallou <[email protected]> +Last-Updated: 19/03/2012 +--- a/INSTALL.Chado ++++ b/INSTALL.Chado +@@ -360,17 +360,17 @@ + the Sequence Ontology (SO) is absolutely required for proper + functioning of the database. The commands to load an ontology are: + +- $ go2fmt.pl -p obo_text -w xml /path/to/obofile | \ ++ $ go2fmt -p obo_text -w xml /path/to/obofile | \ + go-apply-xslt oboxml_to_chadoxml - > obo_text.xml + + This creates a chadoxml file of the obo file - then execute: + +- $ stag-storenode.pl \ ++ $ stag-storenode \ + -d 'dbi:Pg:dbname=$CHADO_DB_NAME;host=$CHADO_DB_HOST;port=$CHADO_DB_PORT' \ + --user $CHADO_DB_USERNAME --password $CHADO_DB_PASSWORD obo_text.xml + + If you have other ontology format files, the commands are similar; +-consult the documentation for go2fmt.pl and go-apply-xslt for your ++consult the documentation for go2fmt and go-apply-xslt for your + file format. + + It is a good idea at this point to make a back up of the database, +--- a/lib/Bio/Chado/Builder.pm ++++ b/lib/Bio/Chado/Builder.pm +@@ -350,7 +350,7 @@ + } + + # loading chadoxml +- my $stag_string = "stag-storenode.pl -d 'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'"; ++ my $stag_string = "stag-storenode -d 'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'"; + $stag_string .= " --user $db_user " if $db_user; + $stag_string .= " --password $db_pass " if $db_pass; + $sys_call = join( ' ', +@@ -387,7 +387,7 @@ + + + $sys_call = join( ' ', +- "stag-storenode.pl -d 'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'", ++ "stag-storenode -d 'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'", + catfile( $conf->{'path'}{'data'}, $deffile->{'local'}.'xml') + ); + Modified: trunk/packages/gmod/chado/trunk/debian/patches/series =================================================================== --- trunk/packages/gmod/chado/trunk/debian/patches/series 2012-03-19 08:53:48 UTC (rev 10022) +++ trunk/packages/gmod/chado/trunk/debian/patches/series 2012-03-19 08:54:49 UTC (rev 10023) @@ -3,3 +3,4 @@ fix_spelling_manpage fix_manpages setBinPathForBuilder +remove_pl_extension.patch _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
