[med-svn] r16512 - trunk/packages/galaxy/trunk/debian
Timothy Booth
tbooth-guest at moszumanska.debian.org
Mon Mar 24 17:34:23 UTC 2014
Author: tbooth-guest
Date: 2014-03-24 17:34:23 +0000 (Mon, 24 Mar 2014)
New Revision: 16512
Removed:
trunk/packages/galaxy/trunk/debian/link_configs_for_hacky_first_run.sh
Modified:
trunk/packages/galaxy/trunk/debian/changelog
trunk/packages/galaxy/trunk/debian/copy_sample_config.sh
trunk/packages/galaxy/trunk/debian/galaxy-server.install
trunk/packages/galaxy/trunk/debian/run.sh
Log:
shed_*conf.xml files are not really conf files, as I see it, since they
are modified by the server. Remove them from conffiles mechanism and
put in /var.
Modified: trunk/packages/galaxy/trunk/debian/changelog
===================================================================
--- trunk/packages/galaxy/trunk/debian/changelog 2014-03-24 16:03:56 UTC (rev 16511)
+++ trunk/packages/galaxy/trunk/debian/changelog 2014-03-24 17:34:23 UTC (rev 16512)
@@ -1,11 +1,13 @@
-galaxy (1.bl.py27.20140210-0biolinux4) precise; urgency=low
+galaxy (1.bl.py27.20140210-0biolinux5) precise; urgency=low
* Fixed misspelling of shed-tools/shed_tools that messed up symlinks
* Don't build galaxy-server-all from this package any more, as the tool
defs are not distributed in the Gaalxy core.
- * Why is this package not building on the PPA?
+ * Initialise just the shed_*.xml configuration files from .sample files
+ on first run, because I don't see that these need to be managed
+ by debconf.
- -- Tim Booth <tbooth at ceh.ac.uk> Mon, 24 Mar 2014 10:49:50 +0000
+ -- Tim Booth <tbooth at ceh.ac.uk> Mon, 24 Mar 2014 16:45:34 +0000
galaxy (1.bl.py27.20140210-0biolinux1) precise; urgency=low
Modified: trunk/packages/galaxy/trunk/debian/copy_sample_config.sh
===================================================================
--- trunk/packages/galaxy/trunk/debian/copy_sample_config.sh 2014-03-24 16:03:56 UTC (rev 16511)
+++ trunk/packages/galaxy/trunk/debian/copy_sample_config.sh 2014-03-24 17:34:23 UTC (rev 16512)
@@ -58,8 +58,11 @@
cp ../universe_wsgi.d/1* "$d"
# Deal with shed_tool*_conf.xml
-for stc in shed_tool_conf.xml shed_tool_data_table_conf.xml ; do
- echo "Initialising /var/lib/galaxy-server/${stc} from ${stc}.sample"
- mv -v usr/lib/galaxy-server/${stc}.sample var/lib/galaxy-server/shed_tools/${stc}
+# These are modified by Galaxy and not manually edited, so belong in /var
+# but we do need the initial versions, so revert to the idea of copying the
+# sample files.
+for stc in shed_tool_conf.xml shed_tool_data_table_conf.xml shed_data_manager_conf.xml ; do
+ echo "Linking to /var/lib/galaxy-server/${stc}, to be initialised from ${stc}.sample"
+ #mv -v usr/lib/galaxy-server/${stc}.sample var/lib/galaxy-server/shed_tools/${stc}
ln -s /var/lib/galaxy-server/shed_tools/${stc} usr/lib/galaxy-server/${stc}
done
Modified: trunk/packages/galaxy/trunk/debian/galaxy-server.install
===================================================================
--- trunk/packages/galaxy/trunk/debian/galaxy-server.install 2014-03-24 16:03:56 UTC (rev 16511)
+++ trunk/packages/galaxy/trunk/debian/galaxy-server.install 2014-03-24 17:34:23 UTC (rev 16512)
@@ -28,8 +28,9 @@
/usr/lib/galaxy-server/tools/
/usr/share/galaxy-server/static/
/usr/share/galaxy-server/templates/
-### I've taken all the .sample files out, as they are copied in /etc
+### I've taken most of the .sample files out, as they are copied in /etc
### and protected by debconf.
+/usr/lib/galaxy-server/shed_*.sample
/usr/lib/galaxy-server/universe_wsgi.d
###Build script creates links to files in /etc/
Deleted: trunk/packages/galaxy/trunk/debian/link_configs_for_hacky_first_run.sh
===================================================================
--- trunk/packages/galaxy/trunk/debian/link_configs_for_hacky_first_run.sh 2014-03-24 16:03:56 UTC (rev 16511)
+++ trunk/packages/galaxy/trunk/debian/link_configs_for_hacky_first_run.sh 2014-03-24 17:34:23 UTC (rev 16512)
@@ -1,38 +0,0 @@
-#!/bin/bash
-
-# This gives us temporary config files
-# for use during the build, and then cleans them up.
-
-if [ $1 == "clean" ] ; then
- #Since there should be no symlinks at this point I can be lazy with the cleanup,
- #but just to be sure, don't touch the debian directory.
- find -path ./debian -prune -or -type l -exec rm '{}' ';'
- exit $?
-fi
-
-SAMPLES="
- community_wsgi.ini.sample
- datatypes_conf.xml.sample
- external_service_types_conf.xml.sample
- migrated_tools_conf.xml.sample
- reports_wsgi.ini.sample
- shed_tool_conf.xml.sample
- tool_conf.xml.sample
- tool_data_table_conf.xml.sample
- tool_sheds_conf.xml.sample
- universe_wsgi.ini.sample
- tool-data/shared/*/*.sample
- tool-data/*.sample
- static/*.sample
-"
-
-#Expand globs in correct directory
-SAMPLES=`( cd . ; echo $SAMPLES )`
-
-# Create any missing config/location files
-for sample in $SAMPLES; do
- file=`echo $sample | sed -e 's/\.sample$//'`
- echo "Linking $file to `basename $sample`"
- ln -sv $sample $file
-done
-
Modified: trunk/packages/galaxy/trunk/debian/run.sh
===================================================================
--- trunk/packages/galaxy/trunk/debian/run.sh 2014-03-24 16:03:56 UTC (rev 16511)
+++ trunk/packages/galaxy/trunk/debian/run.sh 2014-03-24 17:34:23 UTC (rev 16512)
@@ -9,7 +9,7 @@
#Galaxy does expect somewhere to unpack 'eggs'
export PYTHON_EGG_CACHE=/var/lib/galaxy-server/egg-cache
-#This script would normally be called from by upstart from /etc/init/galaxy.conf
+#This script would normally be called by upstart from /etc/init/galaxy.conf
#You can run it manually but be sure to run it as the right user.
RIGHT_USER=`stat -c%U "$PYTHON_EGG_CACHE"`
if ! [ `id -un` = $RIGHT_USER ] ; then
@@ -18,6 +18,18 @@
exit 1
fi
+# Initialise shed_tools files from .sample files. Initial installation will
+# leave dangling symlinks to location under /var.
+# Note integrated_tool_panel.xml has no sample file.
+for sam in *.sample ; do
+ file="`basename "$sam" .sample`"
+
+ if [ -L "$file" -a \! -e "$file" ] ; then
+ echo "Initializing $file from $sam"
+ cat "$sam" > "$file"
+ fi
+done
+
# Make universe_wsgi.ini on-the-fly unless it already exists.
# Hint - you most probably don't ever want to make a monolithic UWINI
# unless you are are doing it for testing purposes.
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