[med-svn] r8068 - in trunk/packages/gmod/chado/trunk/debian: . patches
olivier sallou
osallou-guest at alioth.debian.org
Tue Oct 4 07:39:10 UTC 2011
Author: osallou-guest
Date: 2011-10-04 07:39:10 +0000 (Tue, 04 Oct 2011)
New Revision: 8068
Added:
trunk/packages/gmod/chado/trunk/debian/patches/fix_perl_headers
Removed:
trunk/packages/gmod/chado/trunk/debian/patches/error_message
trunk/packages/gmod/chado/trunk/debian/patches/error_message.patch
trunk/packages/gmod/chado/trunk/debian/patches/fix_log4perl_location
trunk/packages/gmod/chado/trunk/debian/patches/no_tests.patch
Modified:
trunk/packages/gmod/chado/trunk/debian/libchado-perl.dirs
trunk/packages/gmod/chado/trunk/debian/libchado-perl.docs
trunk/packages/gmod/chado/trunk/debian/patches/series
trunk/packages/gmod/chado/trunk/debian/rules
Log:
update to v1.2
Modified: trunk/packages/gmod/chado/trunk/debian/libchado-perl.dirs
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/libchado-perl.dirs 2011-10-03 23:39:19 UTC (rev 8067)
+++ trunk/packages/gmod/chado/trunk/debian/libchado-perl.dirs 2011-10-04 07:39:10 UTC (rev 8068)
@@ -1,3 +1,3 @@
-usr/share/gmod/chado
+usr/share/gmod/chado/bin
etc/gmod
tmp
Modified: trunk/packages/gmod/chado/trunk/debian/libchado-perl.docs
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/libchado-perl.docs 2011-10-03 23:39:19 UTC (rev 8067)
+++ trunk/packages/gmod/chado/trunk/debian/libchado-perl.docs 2011-10-04 07:39:10 UTC (rev 8068)
@@ -1,13 +1,8 @@
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
Deleted: trunk/packages/gmod/chado/trunk/debian/patches/error_message
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/error_message 2011-10-03 23:39:19 UTC (rev 8067)
+++ trunk/packages/gmod/chado/trunk/debian/patches/error_message 2011-10-04 07:39:10 UTC (rev 8068)
@@ -1,18 +0,0 @@
---- a/install_util/conf_install.PLS
-+++ b/install_util/conf_install.PLS
-@@ -64,13 +64,13 @@
- 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=$gmod_root/tmp\n";
- print GMODCONF "VERSION=$version\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";
- }
Deleted: trunk/packages/gmod/chado/trunk/debian/patches/error_message.patch
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/error_message.patch 2011-10-03 23:39:19 UTC (rev 8067)
+++ trunk/packages/gmod/chado/trunk/debian/patches/error_message.patch 2011-10-04 07:39:10 UTC (rev 8068)
@@ -1,17 +0,0 @@
---- a/install_util/conf_install.PLS 2011-07-14 14:53:38.768356998 +0200
-+++ b/install_util/conf_install.PLS 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";
- }
Deleted: trunk/packages/gmod/chado/trunk/debian/patches/fix_log4perl_location
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/fix_log4perl_location 2011-10-03 23:39:19 UTC (rev 8067)
+++ trunk/packages/gmod/chado/trunk/debian/patches/fix_log4perl_location 2011-10-04 07:39:10 UTC (rev 8068)
@@ -1,26 +0,0 @@
---- a/install_util/log4perl.conf.PLS
-+++ b/install_util/log4perl.conf.PLS
-@@ -57,18 +57,18 @@
- log4perl.appender.Turnkey_Render.layout.ConversionPattern =%c - [%d{HH:mm}] %M() in file .../%F{2} (line %L) says: %m%n
- );
-
--if (-e '/etc/log4perl.conf') {
-+if (-e 'debian/libchado-perl/etc/log4perl.conf') {
- warn "\n\nYou appear to already have a log4perl.conf file in /etc\n";
- warn "Append the contents of ./log4perl.conf to your /etc/log4perl.conf.\n";
-
-- open OUT, ">log4perl.conf" or die "unable to open log4perl.conf for writing: $!\n";
-+ open OUT, ">debian/libchado-perl/etc/log4perl.conf" or die "unable to open log4perl.conf for writing: $!\n";
- print OUT $conf_text;
- close OUT;
-- chmod (0666, "log4perl.conf");
-+ chmod (0666, "debian/libchado-perl/etc/log4perl.conf");
-
- } else {
-- warn "Installing log4perl.conf in /etc...\n";
-- open CONF, ">/etc/log4perl.conf" or die "unable to open /etc/log4perl.conf: $!\n";
-+ warn "Installing log4perl.conf in debian/libchado-perl/etc...\n";
-+ open CONF, ">debian/libchado-perl/etc/log4perl.conf" or die "unable to open debian/libchado-perl/etc/log4perl.conf: $!\n";
- print CONF $conf_text;
- close CONF;
- }
Added: trunk/packages/gmod/chado/trunk/debian/patches/fix_perl_headers
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/fix_perl_headers (rev 0)
+++ trunk/packages/gmod/chado/trunk/debian/patches/fix_perl_headers 2011-10-04 07:39:10 UTC (rev 8068)
@@ -0,0 +1,56 @@
+--- a/bin/gmod_bulk_load_pubmed.pl
++++ b/bin/gmod_bulk_load_pubmed.pl
+@@ -1,4 +1,4 @@
+-
++#!/usr/bin/perl
+ =head1 NAME
+
+ gmod_bulk_load_pubmed.pl
+--- a/bin/load_ncbi_taxonomy.pl
++++ b/bin/load_ncbi_taxonomy.pl
+@@ -1,4 +1,4 @@
+-
++#!/usr/bin/perl
+ =head1 NAME
+
+ load_ncbi_taxonomy.pl
+--- a/bin/load_taxonomy_cvterms.pl
++++ b/bin/load_taxonomy_cvterms.pl
+@@ -1,4 +1,4 @@
+-
++#!/usr/bin/perl
+ =head1 NAME
+
+ load_taxonomy_cvterms.pl
+--- a/modules/bin/makedep.pl
++++ b/modules/bin/makedep.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+ #
+ # (c) Hilmar Lapp, hlapp at gmx.net, 2007.
+ #
+--- a/modules/bin/mk.pl
++++ b/modules/bin/mk.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+
+ foreach $f (@ARGV) {
+ open(F,$f) || die("no $f");
+--- a/modules/cv/bridges/bin/create-bridge-sql.pl
++++ b/modules/cv/bridges/bin/create-bridge-sql.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+ use Data::Stag;
+--- a/modules/sequence/bridges/bin/create-sofa-bridge.pl
++++ b/modules/sequence/bridges/bin/create-sofa-bridge.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+
+ use strict;
+
Deleted: trunk/packages/gmod/chado/trunk/debian/patches/no_tests.patch
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/no_tests.patch 2011-10-03 23:39:19 UTC (rev 8067)
+++ trunk/packages/gmod/chado/trunk/debian/patches/no_tests.patch 2011-10-04 07:39:10 UTC (rev 8068)
@@ -1,18 +0,0 @@
-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);
-
- #########################
-
Modified: trunk/packages/gmod/chado/trunk/debian/patches/series
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/series 2011-10-03 23:39:19 UTC (rev 8067)
+++ trunk/packages/gmod/chado/trunk/debian/patches/series 2011-10-04 07:39:10 UTC (rev 8068)
@@ -1,4 +1,2 @@
-no_tests
+fix_perl_headers
force_SIMPLE
-fix_conf_path
-no_chaos.patch
Modified: trunk/packages/gmod/chado/trunk/debian/rules
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/rules 2011-10-03 23:39:19 UTC (rev 8067)
+++ trunk/packages/gmod/chado/trunk/debian/rules 2011-10-04 07:39:10 UTC (rev 8068)
@@ -21,10 +21,15 @@
override_dh_install:
dh_install -O--buildsystem=perl_makemaker
- sed -i 's/SQLFILE=\/.*\/libchado-perl/SQLFILE=/' $(GMOD_ROOT)/conf/gmod-chado.conf
- sed -i 's/TMP=\/.*\/tmp/CONF=\/tmp/' $(GMOD_ROOT)/conf/gmod.conf
- sed -i 's/CONF=.*\/conf/CONF=\/etc\/gmod/' $(GMOD_ROOT)/conf/gmod.conf
- mv $(GMOD_ROOT)/conf/* debian/libchado-perl/etc/gmod/
+ sed -i 's/SQLFILE=\/.*\/libchado-perl/SQLFILE=/' debian/libchado-perl/conf/gmod-chado.conf
+ sed -i 's/TMP=\/.*\/tmp/CONF=\/tmp/' debian/libchado-perl/conf/gmod.conf
+ sed -i 's/CONF=.*\/conf/CONF=\/etc\/gmod/' debian/libchado-perl/conf/gmod.conf
+ #mv $(GMOD_ROOT)/conf/* debian/libchado-perl/etc/gmod/
+ # Give exexution rights to perl scripts
+ find debian/libchado-perl/ -name *.pl | xargs chmod 755
+ mv debian/libchado-perl/usr/bin/* debian/libchado-perl/usr/share/gmod/chado/bin/
+ mv debian/libchado-perl/usr/share/gmod/chado/bin/*.pl debian/libchado-perl/usr/bin/
+ rename 's/\.pl//' debian/libchado-perl/usr/bin/*.pl
override_dh_auto_test:
echo "Not testing."
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