[med-svn] r7743 - in trunk/packages/gmod/chado/trunk/debian: . patches
olivier sallou
osallou-guest at alioth.debian.org
Mon Sep 12 09:07:49 UTC 2011
Author: osallou-guest
Date: 2011-09-12 09:07:49 +0000 (Mon, 12 Sep 2011)
New Revision: 7743
Added:
trunk/packages/gmod/chado/trunk/debian/libchado-perl.links
trunk/packages/gmod/chado/trunk/debian/patches/fix_log4perl_location
trunk/packages/gmod/chado/trunk/debian/patches/force_SIMPLE
trunk/packages/gmod/chado/trunk/debian/postinst
Modified:
trunk/packages/gmod/chado/trunk/debian/changelog
trunk/packages/gmod/chado/trunk/debian/control
trunk/packages/gmod/chado/trunk/debian/libchado-perl.dirs
trunk/packages/gmod/chado/trunk/debian/patches/series
trunk/packages/gmod/chado/trunk/debian/rules
Log:
add patches for install, move conf to /etc
Modified: trunk/packages/gmod/chado/trunk/debian/changelog
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/changelog 2011-09-12 09:06:16 UTC (rev 7742)
+++ trunk/packages/gmod/chado/trunk/debian/changelog 2011-09-12 09:07:49 UTC (rev 7743)
@@ -1,5 +1,7 @@
-libchado-perl (1.12-1) unstable; urgency=low
+libchado-perl (1.11-1) unstable; urgency=low
- * Initial Release.
+ * Initial Release (Closes: #639868).
+ TODO update for 1.12, fix some path issues
+ add SQL install step in postinst
- -- Steffen Moeller <moeller at debian.org> Thu, 14 Jul 2011 12:44:56 +0200
+ -- Olivier Sallou <olivier.sallou at irisa.fr> Thu, 14 Jul 2011 12:44:56 +0200
Modified: trunk/packages/gmod/chado/trunk/debian/control
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/control 2011-09-12 09:06:16 UTC (rev 7742)
+++ trunk/packages/gmod/chado/trunk/debian/control 2011-09-12 09:07:49 UTC (rev 7743)
@@ -2,9 +2,9 @@
Section: perl
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Scott Cain <scain at cpan.org>, Steffen Moeller <moeller at debian.org>
+Uploaders: Scott Cain <scain at cpan.org>, Steffen Moeller <moeller at debian.org>, Olivier Sallou <olivier.sallou at irisa.fr>
Build-Depends: debhelper (>= 8)
-Build-Depends-Indep: perl, libtemplate-perl, libclass-dbi-pg-perl, libclass-dbi-pager-perl, libxml-libxslt-perl
+Build-Depends-Indep: perl, libtemplate-perl, libclass-dbi-pg-perl, libclass-dbi-pager-perl, libxml-libxslt-perl, liblog-log4perl-perl
Standards-Version: 3.9.2
Homepage: http://gmod.org/wiki/Chado
Vcs-Browser: http://svn.debian.org/viewvc/debian-med/trunk/packages/chado/trunk/
@@ -13,6 +13,7 @@
Package: libchado-perl
Architecture: all
Depends: ${misc:Depends}, ${perl:Depends}
+Recommends: xsltproc
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
Modified: trunk/packages/gmod/chado/trunk/debian/libchado-perl.dirs
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/libchado-perl.dirs 2011-09-12 09:06:16 UTC (rev 7742)
+++ trunk/packages/gmod/chado/trunk/debian/libchado-perl.dirs 2011-09-12 09:07:49 UTC (rev 7743)
@@ -1 +1,3 @@
usr/share/gmod/chado
+etc/gmod
+tmp
Added: trunk/packages/gmod/chado/trunk/debian/libchado-perl.links
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/libchado-perl.links (rev 0)
+++ trunk/packages/gmod/chado/trunk/debian/libchado-perl.links 2011-09-12 09:07:49 UTC (rev 7743)
@@ -0,0 +1,2 @@
+etc/gmod/gmod.conf usr/share/gmod/chado/conf/gmod.conf
+etc/gmod/gmod-chado.conf usr/share/gmod/chado/conf/gmod-chado.conf
Added: trunk/packages/gmod/chado/trunk/debian/patches/fix_log4perl_location
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/fix_log4perl_location (rev 0)
+++ trunk/packages/gmod/chado/trunk/debian/patches/fix_log4perl_location 2011-09-12 09:07:49 UTC (rev 7743)
@@ -0,0 +1,26 @@
+--- 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/force_SIMPLE
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/force_SIMPLE (rev 0)
+++ trunk/packages/gmod/chado/trunk/debian/patches/force_SIMPLE 2011-09-12 09:07:49 UTC (rev 7743)
@@ -0,0 +1,16 @@
+--- a/Makefile.PL
++++ b/Makefile.PL
+@@ -234,9 +234,10 @@
+ my ( $DBDRIVER, $DBNAME, $DBUSER, $DBPASS, $DBHOST, $DBPORT,
+ $SQLFILES, $EXTERNAL_DDL, $LOCAL_TMP, $DBORGANISM, $APOLLO, $DEFAULT);
+
+-$O{'SIMPLE'} = prompt(
+- "Use the simple install (uses default database schema, which contains\nall of the modules and extensions to the schema and all of the non-trigger functions.\nThis is probably what you want)", 'Y'
+- );
++#$O{'SIMPLE'} = prompt(
++# "Use the simple install (uses default database schema, which contains\nall of the modules and extensions to the schema and all of the non-trigger functions.\nThis is probably what you want)", 'Y'
++# );
++$O{'SIMPLE'} = "Y";
+
+ if ( ! @argv && %conf ) {
+ my $answer = prompt(
Modified: trunk/packages/gmod/chado/trunk/debian/patches/series
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/series 2011-09-12 09:06:16 UTC (rev 7742)
+++ trunk/packages/gmod/chado/trunk/debian/patches/series 2011-09-12 09:07:49 UTC (rev 7743)
@@ -1,3 +1,6 @@
error_message.patch
no_tests.patch
+fix_log4perl_location
+force_SIMPLE
+fix_conf_path
no_chaos.patch
Added: trunk/packages/gmod/chado/trunk/debian/postinst
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/postinst (rev 0)
+++ trunk/packages/gmod/chado/trunk/debian/postinst 2011-09-12 09:07:49 UTC (rev 7743)
@@ -0,0 +1,20 @@
+#!/bin/bash
+
+set -e
+
+case "$1" in
+ configure)
+ ;;
+
+ abort-upgrade|abort-remove|abort-deconfigure)
+ ;;
+
+ *)
+ echo "postinst called with unknown argument \`$1'" >&2
+ exit 1
+ ;;
+esac
+
+
+#DEBHELPER#
+
Modified: trunk/packages/gmod/chado/trunk/debian/rules
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/rules 2011-09-12 09:06:16 UTC (rev 7742)
+++ trunk/packages/gmod/chado/trunk/debian/rules 2011-09-12 09:07:49 UTC (rev 7743)
@@ -17,7 +17,14 @@
dh $@ --buildsystem=perl_makemaker
override_dh_auto_configure:
- perl Makefile.PL INSTALL_BASE=/usr
+ perl Makefile.PL INSTALL_BASE=/usr DBNAME=$(CHADO_DB_NAME) DBUSER=chado DBPASSWORD=chado DBHOST=localhost DBPORT=5432 GMOD_ROOT=$(GMOD_ROOT) DBDRIVER=PostgreSQL RECONFIGURE=1 SIMPLE=Y LOCAL_TMP=/tmp
+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/
+
override_dh_auto_test:
echo "Not testing."
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