[med-svn] r18710 - in trunk/packages/galaxy/trunk/debian: . apache-proxy-files/etc/galaxy-server apache-proxy-files/usr/share/galaxy-server apache-proxy-files/usr/share/galaxy-server/logout apache-proxy-files/usr/share/galaxy-server/static config_override patches universe_wsgi.d
Timothy Booth
tbooth-guest at moszumanska.debian.org
Sun Feb 1 13:04:22 UTC 2015
Author: tbooth-guest
Date: 2015-02-01 13:04:21 +0000 (Sun, 01 Feb 2015)
New Revision: 18710
Added:
trunk/packages/galaxy/trunk/debian/apache-proxy-files/usr/share/galaxy-server/static/
trunk/packages/galaxy/trunk/debian/apache-proxy-files/usr/share/galaxy-server/static/logout1.html
trunk/packages/galaxy/trunk/debian/cleanup_everything.sh
trunk/packages/galaxy/trunk/debian/config_override/tool_data_table_conf.xml
trunk/packages/galaxy/trunk/debian/galaxy-server.preinst
trunk/packages/galaxy/trunk/debian/patches/add_favicon_to_masthead
trunk/packages/galaxy/trunk/debian/patches/commit_1298d3f
trunk/packages/galaxy/trunk/debian/patches/fix_build_universe_config
trunk/packages/galaxy/trunk/debian/patches/fix_workflow_misconfiguration_report
Modified:
trunk/packages/galaxy/trunk/debian/apache-proxy-files/etc/galaxy-server/galaxy.htaccess
trunk/packages/galaxy/trunk/debian/apache-proxy-files/usr/share/galaxy-server/logout/.htaccess
trunk/packages/galaxy/trunk/debian/changelog
trunk/packages/galaxy/trunk/debian/config_override/welcome.html
trunk/packages/galaxy/trunk/debian/control
trunk/packages/galaxy/trunk/debian/copy_sample_config.sh
trunk/packages/galaxy/trunk/debian/galaxy-server-apache-proxy.postinst
trunk/packages/galaxy/trunk/debian/galaxy-server-apache-proxy.postrm
trunk/packages/galaxy/trunk/debian/galaxy-server-pg-database.postinst
trunk/packages/galaxy/trunk/debian/galaxy-server-pg-database.postrm
trunk/packages/galaxy/trunk/debian/galaxy-server.install
trunk/packages/galaxy/trunk/debian/galaxy-server.postinst
trunk/packages/galaxy/trunk/debian/make_transfer_dirs.sh
trunk/packages/galaxy/trunk/debian/patches/relax_password_length_restriction
trunk/packages/galaxy/trunk/debian/patches/series
trunk/packages/galaxy/trunk/debian/patches/shed_tools_data_path
trunk/packages/galaxy/trunk/debian/patches/tell_user_how_to_add_administrator
trunk/packages/galaxy/trunk/debian/patches/use_system_python_libs
trunk/packages/galaxy/trunk/debian/rules
trunk/packages/galaxy/trunk/debian/run.sh
trunk/packages/galaxy/trunk/debian/universe_wsgi.d/31_apache-proxy.ini
Log:
Latest batch of changes to the package - still a long long way from Debian compliance.
Modified: trunk/packages/galaxy/trunk/debian/apache-proxy-files/etc/galaxy-server/galaxy.htaccess
===================================================================
--- trunk/packages/galaxy/trunk/debian/apache-proxy-files/etc/galaxy-server/galaxy.htaccess 2015-02-01 13:03:34 UTC (rev 18709)
+++ trunk/packages/galaxy/trunk/debian/apache-proxy-files/etc/galaxy-server/galaxy.htaccess 2015-02-01 13:04:21 UTC (rev 18710)
@@ -27,13 +27,12 @@
<ul><li><code>sudo usermod -aG galaxy user1</code></ul></li>\
</html>"
-# You may want to comment these 2 lines out or to
+# You may want to comment this line out or to
# change the group required, but users still need to
# be in the galaxy group for SFTP uploads to work properly.
-AuthzUnixgroup on
-Require group galaxy
+Require unix-group galaxy
-# This is needed to tell Galaxy about the remote
-# user.
+# This is needed to tell Galaxy about the remote user, but after the
+# initial login Galaxy uses the galaxysession cookie to identify the session.
RequestHeader set REMOTE_USER %{RU}e env=RU
RequestHeader unset Authorization env=RU
Modified: trunk/packages/galaxy/trunk/debian/apache-proxy-files/usr/share/galaxy-server/logout/.htaccess
===================================================================
--- trunk/packages/galaxy/trunk/debian/apache-proxy-files/usr/share/galaxy-server/logout/.htaccess 2015-02-01 13:03:34 UTC (rev 18709)
+++ trunk/packages/galaxy/trunk/debian/apache-proxy-files/usr/share/galaxy-server/logout/.htaccess 2015-02-01 13:04:21 UTC (rev 18710)
@@ -6,3 +6,8 @@
AuthUserFile /usr/share/galaxy-server/logout/.htpasswd
Require user logout
+
+# This assumes that the session cookie is "galaxysession" and it also assumes that
+# something will be loaded from the server, and not just pulled from the cache. The
+# javascript in logout1.html tries to make sure this happens.
+Header set Set-Cookie "galaxysession=00000000; path=/; expires=Thu, 01 Jan 1970 00:00:00 GMT"
Added: trunk/packages/galaxy/trunk/debian/apache-proxy-files/usr/share/galaxy-server/static/logout1.html
===================================================================
--- trunk/packages/galaxy/trunk/debian/apache-proxy-files/usr/share/galaxy-server/static/logout1.html (rev 0)
+++ trunk/packages/galaxy/trunk/debian/apache-proxy-files/usr/share/galaxy-server/static/logout1.html 2015-02-01 13:04:21 UTC (rev 18710)
@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <!-- This should be served as galaxy/logout1.html, not /galaxy/static/logout1.html -->
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <link rel="stylesheet" href="static/style/base.css" type="text/css" />
+ <title>Logging out</title>
+
+<script type="text/javascript">
+
+ var r=new XMLHttpRequest();
+ //Force the request to not cache.
+ var target='logout.html?' + new Date().getTime();
+
+ r.onreadystatechange=function(){
+ if(r.readyState==4)window.location.replace(target)
+ };
+ r.open('get',target,true,'logout','logout');
+ r.send();
+</script>
+
+</head>
+<body>
+ <div class="document">
+ <div class="donemessagelarge">
+ <strong>Logging out...</strong>
+ <hr>
+ This should take at most a couple of seconds.
+ </div>
+ <br/>
+</body>
+</html>
Modified: trunk/packages/galaxy/trunk/debian/changelog
===================================================================
--- trunk/packages/galaxy/trunk/debian/changelog 2015-02-01 13:03:34 UTC (rev 18709)
+++ trunk/packages/galaxy/trunk/debian/changelog 2015-02-01 13:04:21 UTC (rev 18710)
@@ -1,13 +1,80 @@
+galaxy (1.bl.py27.20140730-0biolinux4) trusty; urgency=medium
+
+ * Added default-jre as a build dep, to fix repacking of javascript
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Tue, 19 Aug 2014 17:16:56 +0100
+
+galaxy (1.bl.py27.20140730-0biolinux2) trusty; urgency=medium
+
+ * Update to 20140730 in the hope this supports the new data manager
+ tools system.
+ - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071198/pdf/btu119.pdf
+ * Drop the upstream patch as this is now integrated.
+ * Fix apache-proxy to work with new Apache a2enconf system
+ * Use new syntax for AuthzUnixgroup in .htaccess
+ * Add DirectoryIndex '' to galaxy.conf
+ * Remove link to silly noodle image no longer included
+ * Move tool-data out to /var/lib/galaxy-server and fix in preinst too
+ to allow new data manager shed tools to work
+ * Made shed_tools and tool-data world readable to aid debugging, as
+ there is no reason to hide them
+ * Re-re-fix the logout hack so we always defeat the Galaxy session cookie
+ * Link to documentation on environmentalomics.org
+ * Tweak the cleanup script to be more friendly (TODO: make it run weekly)
+ * Fudge PYTHONPATH in run.sh to enable bx-python, needed by genomic interval
+ tools
+ * Force repack of all .js files on build
+ * Patch mako templates to ensure favicon appears in browser title bar
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Wed, 06 Aug 2014 14:26:55 +0100
+
+galaxy (1.bl.py27.20140210-0biolinux8.2) trusty; urgency=medium
+
+ * Stop debian/galaxy-server-pg-database.postinst from complaining about new
+ pg_lsclusters output.
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Fri, 27 Jun 2014 16:56:31 +0100
+
+galaxy (1.bl.py27.20140210-0biolinux8.1) trusty; urgency=low
+
+ * Rebuild for Trusty
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Tue, 10 Jun 2014 14:12:27 +0100
+
+galaxy (1.bl.py27.20140210-0biolinux8) precise; urgency=low
+
+ * Fix silly error in make_transfer_dirs.sh
+ * Add new cleanup_everything.sh script
+ * Added patch https://bitbucket.org/galaxy/galaxy-central/commits/1298d3f
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Thu, 29 May 2014 17:27:47 +0100
+
+galaxy (1.bl.py27.20140210-0biolinux6) precise; urgency=low
+
+ * Fixed basic_auth logout once more. Slightly neater now anyway.
+ * Made apache-proxy and pg-database remove their config files on removal so
+ you don't have to remember to purge them.
+ * Made config files in /tmp group-readable.
+ * Added data_manager_conf.xml.sample to list of sample files to copy
+ * Activate xz packing for drastic size reduction, and fix a couple of
+ Lintian warnings.
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Wed, 02 Apr 2014 16:46:49 +0100
+
galaxy (1.bl.py27.20140210-0biolinux5) precise; urgency=low
- * Fixed misspelling of shed-tools/shed_tools that messed up symlinks
+ * 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.
+ defs are not distributed in the Galaxy core.
* 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.
+ on first run, because I don't see that these should be be managed
+ by debconf - they are basically used as a config DB by Galaxy.
+ * Use overridden custom version of tool_data_table_conf.xml until I can work
+ out how to split this into multiple files or else build the config
+ on-the-fly. Really this should be in bl_tools package.
+ * Remove .svn folders that had crept into debs
- -- Tim Booth <tbooth at ceh.ac.uk> Mon, 24 Mar 2014 16:45:34 +0000
+ -- Tim Booth <tbooth at ceh.ac.uk> Thu, 27 Mar 2014 17:17:26 +0000
galaxy (1.bl.py27.20140210-0biolinux1) precise; urgency=low
@@ -34,7 +101,7 @@
* Now realised that Galaxy will use local libs if it finds the
local version is just right. And it won't fetch those eggs.
- Oh. Why does it have to be so "clever"?
+ Oh. Why does it have to be so "clever"?
For now, just ensure this is built on a machine without
python-migrate installed.
* Reduced use_system_python_libs to just localise psycopg for now,
@@ -48,7 +115,7 @@
it to be reconstructed under /tmp
* Remove old universe_wsgi.ini on upgrade
* Fix and improve galaxy-add-administrator script
- * Be more careful with initctl restart in scripts as it only works
+ * Be more careful with initctl restart in scripts as it only works
when the service was already running.
* Ensure cleanup on purge.
* Added Simon W. Credit to welcome.html
@@ -78,7 +145,7 @@
galaxy (1.bl.py27.20130812-0biolinux2) precise; urgency=low
* Added galaxy-server-pg-database package to set up PG
- * Fixed dep on Bowtie2
+ * Fixed dep on Bowtie2
* Dropped patch dont_fetch_eggs in favour of custom run script
* This upgrades the database before running Galaxy - otherwise
in tests I got unexpected failures. Less hassle for users but
@@ -100,7 +167,7 @@
* New upstream, and more
* Refreshed patches
* Forced Galaxy to accept using LOCAL libs instead of its own
- eggs.
+ eggs.
-- Tim Booth <tbooth at ceh.ac.uk> Thu, 18 Jul 2013 13:39:01 +0100
@@ -126,7 +193,7 @@
* Patch and permissions changes to get run_unit_tests.sh
to work.
- * Moved logs to new location and allowed update script to
+ * Moved logs to new location and allowed update script to
shift them if necessary.
-- Tim Booth <tbooth at ceh.ac.uk> Fri, 12 Oct 2012 17:41:41 +0100
@@ -166,7 +233,7 @@
* Customised welcome.html
* Set arch on all packages to amd64 so as not to upset PPA build
* Modified init script to set environment
- * Changed dependencies of (-all) to match Soon's latest list
+ * Changed dependencies of (-all) to match Soon's latest list
-- Tim Booth <tbooth at ceh.ac.uk> Thu, 03 May 2012 18:19:57 +0100
Added: trunk/packages/galaxy/trunk/debian/cleanup_everything.sh
===================================================================
--- trunk/packages/galaxy/trunk/debian/cleanup_everything.sh (rev 0)
+++ trunk/packages/galaxy/trunk/debian/cleanup_everything.sh 2015-02-01 13:04:21 UTC (rev 18710)
@@ -0,0 +1,105 @@
+#!/bin/bash
+
+# A script to run all the various cleanup routines as recommended in
+# https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets
+
+PRESERVE_DAYS=${PRESERVE_DAYS:-10}
+FORCE=${FORCE:-}
+
+export PYTHON_EGG_CACHE=/var/lib/galaxy-server/egg-cache
+
+# Help me make the log readable...
+LOGFILE=/var/log/galaxy/cleanup_everything.log
+lpre() {
+ if [ "$1" = "" ] || [ "$1" = "-" ] ; then
+ pre=
+ elif [ "$1" = '!' ] ; then
+ pre="**** "
+ else
+ pre="$1=> "
+ fi
+ echo -n "$pre"
+}
+
+log() {
+ pre="`lpre "$1"`"
+ shift
+
+ echo "$pre$@" | tee -a "$LOGFILE"
+}
+
+lcmd() {
+ pre="`lpre "$1"`"
+ spre="`echo "$pre" | sed -e 's/[\/&]/\\&/g'`"
+ shift
+
+ echo "${pre}CMD: $@ ===>" | tee -a "$LOGFILE"
+ if [ -n "$pre" ] ; then
+ eval "$@" | sed "s/^/$spre/" | tee -a "$LOGFILE"
+ else
+ eval "$@" | tee -a "$LOGFILE"
+ fi
+}
+
+# First, ensure I'm running as the same user who owns /var/lib/galaxy-server/egg-cache
+G_USER="`stat -c%U "$PYTHON_EGG_CACHE"`"
+
+if [ "$G_USER" != `whoami` ] ; then
+ echo "You need to run this script as $G_USER. Ie. try: sudo -u $G_USER $0"
+ exit 1
+fi
+
+# Then ensure I'm in the right directory
+if ! cd "/usr/lib/galaxy-server" ; then
+ echo "You need to run this script in /usr/lib/galaxy-server"
+ exit 1
+fi
+
+# Then, make myself a config file - copied from run.sh
+UWINI=universe_wsgi.ini
+RMUWINI=0
+
+if [ ! -e "$UWINI" ] ; then
+ UWINI=`mktemp --tmpdir universe_wsgi_XXXX.ini`
+ python ./scripts/build_universe_config.py universe_wsgi.d/ "$UWINI"
+ chmod g+r "$UWINI"
+ RMUWINI=1
+fi
+
+# === OK, the actual cleanupping ===
+
+log '!' "Cleanup run at `date`"
+
+log duh "delete_userless_histories"
+lcmd duh python ./scripts/cleanup_datasets/cleanup_datasets.py "$UWINI" -d $PRESERVE_DAYS -1
+
+log ph "purge_histories"
+lcmd ph python ./scripts/cleanup_datasets/cleanup_datasets.py "$UWINI" -d $PRESERVE_DAYS -2 -r
+
+log pd "purge_datasets"
+lcmd pd python ./scripts/cleanup_datasets/cleanup_datasets.py "$UWINI" -d $PRESERVE_DAYS -3 -r
+
+log pf "purge_folders"
+lcmd pf python ./scripts/cleanup_datasets/cleanup_datasets.py "$UWINI" -d $PRESERVE_DAYS -5 -r
+
+log pl "purge_libraries"
+lcmd pl python ./scripts/cleanup_datasets/cleanup_datasets.py "$UWINI" -d $PRESERVE_DAYS -4 -r
+
+log dd "delete_datasets"
+lcmd dd python ./scripts/cleanup_datasets/cleanup_datasets.py "$UWINI" -d $PRESERVE_DAYS -6 -r
+
+if [ -n "$FORCE" ] ; then
+ log pd2 "purge_datasets_2 (this time with the -f flag)"
+ lcmd pd2 python ./scripts/cleanup_datasets/cleanup_datasets.py "$UWINI" -d $PRESERVE_DAYS -3 -r -f
+fi
+
+log du "set_user_disk_usage"
+lcmd du env PYTHONPATH=./lib ./scripts/set_user_disk_usage.py -c "$UWINI" 2>&1
+
+log '!' "Finished at `date`"
+
+# === Done. ===
+
+if [ "$RMUWINI" = 1 ] ; then
+ rm "$UWINI"
+fi
Property changes on: trunk/packages/galaxy/trunk/debian/cleanup_everything.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/galaxy/trunk/debian/config_override/tool_data_table_conf.xml
===================================================================
--- trunk/packages/galaxy/trunk/debian/config_override/tool_data_table_conf.xml (rev 0)
+++ trunk/packages/galaxy/trunk/debian/config_override/tool_data_table_conf.xml 2015-02-01 13:04:21 UTC (rev 18710)
@@ -0,0 +1,129 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+ <!-- Locations of all fasta files under genome directory -->
+ <table name="all_fasta" comment_char="#">
+ <columns>value, dbkey, name, path</columns>
+ <file path="tool-data/all_fasta.loc" />
+ </table>
+ <!-- Locations of indexes in the BFAST mapper format -->
+ <table name="bfast_indexes" comment_char="#">
+ <columns>value, dbkey, formats, name, path</columns>
+ <file path="tool-data/bfast_indexes.loc" />
+ </table>
+ <!-- Locations of nucleotide (mega)blast databases -->
+ <table name="blastdb" comment_char="#">
+ <columns>value, name, path</columns>
+ <file path="tool-data/blastdb.loc" />
+ </table>
+ <!-- Locations of protein (mega)blast databases -->
+ <table name="blastdb_p" comment_char="#">
+ <columns>value, name, path</columns>
+ <file path="tool-data/blastdb_p.loc" />
+ </table>
+ <!-- Locations of indexes in the Bowtie2 mapper format -->
+ <table name="bowtie2_indexes" comment_char="#">
+ <columns>value, dbkey, name, path</columns>
+ <file path="tool-data/bowtie2_indices.loc" />
+ </table>
+ <!-- Locations of indexes in the BWA mapper format -->
+ <table name="bwa_indexes" comment_char="#">
+ <columns>value, dbkey, name, path</columns>
+ <file path="tool-data/bwa_index.loc" />
+ </table>
+ <!-- Locations of indexes in the BWA color-space mapper format -->
+ <table name="bwa_indexes_color" comment_char="#">
+ <columns>value, dbkey, name, path</columns>
+ <file path="tool-data/bwa_index_color.loc" />
+ </table>
+ <!-- Locations of MAF files that have been indexed with bx-python -->
+ <table name="indexed_maf_files">
+ <columns>name, value, dbkey, species</columns>
+ <file path="tool-data/maf_index.loc" />
+ </table>
+ <!-- Locations of fasta files appropriate for NGS simulation -->
+ <table name="ngs_sim_fasta" comment_char="#">
+ <columns>value, dbkey, name, path</columns>
+ <file path="tool-data/ngs_sim_fasta.loc" />
+ </table>
+ <!-- Locations of PerM base index files -->
+ <table name="perm_base_indexes" comment_char="#">
+ <columns>value, name, path</columns>
+ <file path="tool-data/perm_base_index.loc" />
+ </table>
+ <!-- Locations of PerM color-space index files -->
+ <table name="perm_color_indexes" comment_char="#">
+ <columns>value, name, path</columns>
+ <file path="tool-data/perm_color_index.loc" />
+ </table>
+ <!-- Location of SAMTools indexes and other files (new version)
+ Warning: until Galaxy release_2013.06.03 the format of this
+ table was:
+
+ <columns>line_type, value, path</columns>
+ <file path="tool-data/sam_fa_indices.loc" />
+
+ If you are updating your tool_data_table_conf.xml to the current
+ version you should first migrate your
+ tool-data/sam_fa_indices.loc file to a new
+ tool-data/sam_fa_new_indices.loc file with the format specified
+ below, which is explained in the relative sample file
+ tool-data/sam_fa_new_indices.loc.sample .
+ By using the new format it is possible to let the user choose
+ among multiple indexed genome variants having the same dbkey,
+ e.g. hg19canon vs. hg19full variants for hg19 dbkey.
+ -->
+ <table name="sam_fa_indexes" comment_char="#">
+ <columns>value, dbkey, name, path</columns>
+ <file path="tool-data/sam_fa_new_indices.loc" />
+ </table>
+ <!-- Location of Picard dict file and other files -->
+ <table name="picard_indexes" comment_char="#">
+ <columns>value, dbkey, name, path</columns>
+ <file path="tool-data/picard_index.loc" />
+ </table>
+ <!-- Location of Picard dict files valid for GATK -->
+ <table name="gatk_picard_indexes" comment_char="#">
+ <columns>value, dbkey, name, path</columns>
+ <file path="tool-data/gatk_sorted_picard_index.loc" />
+ </table>
+ <!-- Available of GATK references -->
+ <table name="gatk_annotations" comment_char="#">
+ <columns>value, name, gatk_value, tools_valid_for</columns>
+ <file path="tool-data/gatk_annotations.txt" />
+ </table>
+ <!-- Location of SRMA dict file and other files -->
+ <table name="srma_indexes" comment_char="#">
+ <columns>value, dbkey, name, path</columns>
+ <file path="tool-data/picard_index.loc" />
+ </table>
+ <!-- Locations of indexes in the Bowtie mapper format for TopHat to use -->
+ <table name="tophat_indexes" comment_char="#">
+ <columns>value, dbkey, name, path</columns>
+ <file path="tool-data/bowtie_indices.loc" />
+ </table>
+ <!-- Locations of indexes in the Bowtie color-space mapper format for TopHat to use -->
+ <table name="tophat_indexes_color" comment_char="#">
+ <columns>value, dbkey, name, path</columns>
+ <file path="tool-data/bowtie_indices_color.loc" />
+ </table>
+ <!-- Locations of indexes in the Bowtie2 mapper format for TopHat2 to use -->
+ <table name="tophat2_indexes" comment_char="#">
+ <columns>value, dbkey, name, path</columns>
+ <file path="tool-data/bowtie2_indices.loc" />
+ </table>
+ <!-- Locations of configurations in the CCAT peak/region caller format -->
+ <table name="ccat_configurations" comment_char="#">
+ <columns>value, name, path</columns>
+ <file path="tool-data/ccat_configurations.loc" />
+ </table>
+ <!-- Location of Mosaik files -->
+ <table name="mosaik_indexes" comment_char="#">
+ <columns>value, dbkey, name, path</columns>
+ <file path="tool-data/mosaik_index.loc" />
+ </table>
+ <!-- Added manually for cufflinks but really belongs in the galaxy-tools-bl package -->
+ <table name="fasta_indexes" comment_char="#">
+ <columns>value, dbkey, name, path</columns>
+ <file path="tool-data/fasta_indexes.loc" />
+ </table>
+</tables>
Modified: trunk/packages/galaxy/trunk/debian/config_override/welcome.html
===================================================================
--- trunk/packages/galaxy/trunk/debian/config_override/welcome.html 2015-02-01 13:03:34 UTC (rev 18709)
+++ trunk/packages/galaxy/trunk/debian/config_override/welcome.html 2015-02-01 13:04:21 UTC (rev 18710)
@@ -10,12 +10,17 @@
<div class="donemessagelarge">
<strong>This is the Galaxy server, packaged for Bio-Linux.</strong>
<hr>
- To customize this page edit <code>/etc/galaxy/static/welcome.html</code> then <code>sudo restart galaxy</code>.
+ To customize this page edit <code>/etc/galaxy-server/static/welcome.html</code> then <code>sudo restart galaxy</code>.
</div>
<br/>
- To find out more about Galaxy, <a target="_blank" href="http://wiki.g2.bx.psu.edu/Learn"/>start here.
+ <strong>For more information about Galaxy on Bio-Linux, <a target="_blank" href="http://environmentalomics.org/bio-linux-galaxy"/>read this page.</a></strong>
+ <br/>
+ <br/>
+ To find out more about Galaxy, <a target="_blank" href="http://wiki.g2.bx.psu.edu/Learn"/>start here.</a>
<br/>
+ <!-- TODO, dd something here now the noodles is dead
<img src="images/noodles.png" alt="WWFSMD?" style="display: block; margin-left: auto; margin-right: auto;" /></a>
+ -->
<hr/>
This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>.
<br/> <br/>
Modified: trunk/packages/galaxy/trunk/debian/control
===================================================================
--- trunk/packages/galaxy/trunk/debian/control 2015-02-01 13:03:34 UTC (rev 18709)
+++ trunk/packages/galaxy/trunk/debian/control 2015-02-01 13:04:21 UTC (rev 18710)
@@ -3,7 +3,8 @@
Section: science
Maintainer: Tim Booth <tbooth at ceh.ac.uk>
Uploaders: H. Soon Gweon <soonio at gmail.com>
-Build-depends: xmlstarlet, python, quilt (>= 0.46-7~), debhelper (>= 8)
+Build-depends: xmlstarlet, python, quilt (>= 0.46-7~), debhelper (>= 8),
+ default-jre
Standards-Version: 3.9.3
Homepage: http://galaxy.psu.edu/
@@ -29,7 +30,7 @@
Package: galaxy-server-pg-database
Architecture: amd64
-Depends: galaxy-server (= ${binary:Version}), python-psycopg2
+Depends: galaxy-server (= ${binary:Version}), python-psycopg2, ${misc:Depends}
Pre-Depends: postgresql | postgresql-8.4
Description: Activates PostgreSQL database back-end for Galaxy
This is a convenience package that attempts to set up Galaxy to use a
@@ -51,7 +52,7 @@
Package: galaxy-server-apache-proxy
Architecture: amd64
Pre-Depends: apache2
-Depends: galaxy-server (= ${binary:Version}), libapache2-mod-authnz-external, libapache2-mod-authz-unixgroup, pwauth
+Depends: galaxy-server (= ${binary:Version}), libapache2-mod-authnz-external, libapache2-mod-authz-unixgroup, pwauth, ${misc:Depends}
Description: Activates Apache2 proxy for Galaxy server, and PAM authentication
This is a convenience package that sets up the Galaxy server to proxy via
Apache2 and changes the authentication to validate users with their regular
Modified: trunk/packages/galaxy/trunk/debian/copy_sample_config.sh
===================================================================
--- trunk/packages/galaxy/trunk/debian/copy_sample_config.sh 2015-02-01 13:03:34 UTC (rev 18709)
+++ trunk/packages/galaxy/trunk/debian/copy_sample_config.sh 2015-02-01 13:04:21 UTC (rev 18710)
@@ -15,6 +15,7 @@
SAMPLES="
datatypes_conf.xml.sample
+ data_manager_conf.xml.sample
external_service_types_conf.xml.sample
migrated_tools_conf.xml.sample
reports_wsgi.ini.sample
Modified: trunk/packages/galaxy/trunk/debian/galaxy-server-apache-proxy.postinst
===================================================================
--- trunk/packages/galaxy/trunk/debian/galaxy-server-apache-proxy.postinst 2015-02-01 13:03:34 UTC (rev 18709)
+++ trunk/packages/galaxy/trunk/debian/galaxy-server-apache-proxy.postinst 2015-02-01 13:04:21 UTC (rev 18710)
@@ -11,13 +11,18 @@
# 4 - Reload Apache2 config and Galaxy
#
-# DEBHELPER #
+#DEBHELPER#
# TODO - on failure, show error via Debconf rather than dumping to terminal.
+ifile="/etc/galaxy-server/universe_wsgi.d/31_apache-proxy.ini";
+if [ -e "$ifile.dpkg-bak" -a \! -e "$ifile" ] ; then
+ mv "$ifile.dpkg-bak" "$ifile"
+fi
+
if [ -n "$1" -a "$1" != "configure" ] ; then
- #Nowt to do.
- #I don't care about abort-deconfigure right now.
+ #Nowt more to do.
+ #I don't care much about abort-deconfigure right now.
exit 0
fi
@@ -32,6 +37,13 @@
exit 1
fi
+# 1a - Also activate the two config fragments. These will be disabled on
+# removal of the package
+if ! a2enconf galaxy pwauth ; then
+ echo "Failed to activate configuration fragments."
+ exit 1
+fi
+
# 2
getent group galaxy >/dev/null || addgroup galaxy
Modified: trunk/packages/galaxy/trunk/debian/galaxy-server-apache-proxy.postrm
===================================================================
--- trunk/packages/galaxy/trunk/debian/galaxy-server-apache-proxy.postrm 2015-02-01 13:03:34 UTC (rev 18709)
+++ trunk/packages/galaxy/trunk/debian/galaxy-server-apache-proxy.postrm 2015-02-01 13:04:21 UTC (rev 18710)
@@ -2,6 +2,8 @@
set -e
set -u
+#DEBHELPER#
+
# I can't deactivate the Apache modules as I have no way to know if the user
# wanted them anyway. But I will remove the galaxy group if it is unused.
@@ -13,11 +15,21 @@
echo "$g_line" | cut -d: -f4 | tr , ' '
}
-# 2
+# Remove unused group
[ -n "`members galaxy`" ] || groupdel galaxy || true
-# 3
-# Already done by installation of config fragment
+# Ensure we no loger see the config fragment
+if [ "$1" = purge ] ; then
+ rm -f /etc/galaxy-server/universe_wsgi.d/31_apache-proxy.ini.dpkg-bak
+elif [ "$1" = remove ] ; then
+ ( cd /etc/galaxy-server/universe_wsgi.d && \
+ mv 31_apache-proxy.ini 31_apache-proxy.ini.dpkg-bak ) || true
+fi
-# 4 - Bounce Apache2 and Galaxy, if it's running
+# Deconfigure Apache config fragments
+a2disconf galaxy pwauth || true
+
+# Bounce Apache2 and Galaxy, if it's running
+invoke-rc.d apache2 reload || true
invoke-rc.d galaxy restart || true
+
Modified: trunk/packages/galaxy/trunk/debian/galaxy-server-pg-database.postinst
===================================================================
--- trunk/packages/galaxy/trunk/debian/galaxy-server-pg-database.postinst 2015-02-01 13:03:34 UTC (rev 18709)
+++ trunk/packages/galaxy/trunk/debian/galaxy-server-pg-database.postinst 2015-02-01 13:04:21 UTC (rev 18710)
@@ -10,7 +10,10 @@
# 4- Modify Galaxy configuration
# 5- Restart Galaxy
-# No hook for debhelper - this is a Perl script!
+#Ignore Debhelper tag - this is a Perl script.
+scalar('
+#DEBHELPER#
+');
# And I don't know if this could be done with dbconfig-common but I'm pretty sure
# how I want to handle things.
@@ -22,9 +25,16 @@
my $DBNAME = $USERNAME;
# Note if you do change this you also need to edit 32_pg-database.ini
+# In any case, ensure the .ini file is in place.
+my $ifile = "/etc/galaxy-server/universe_wsgi.d/32_pg-database.ini";
+if( -e "$ifile.dpkg-bak" && !-e $ifile )
+{
+ rename("$ifile.dpkg-bak", $ifile) or die $!;
+}
+
if( $ARGV[0] && $ARGV[0] ne "configure")
{
- #Nowt to do.
+ #Nowt more to do.
#I don't care about abort-deconfigure right now.
exit 0;
}
@@ -34,7 +44,7 @@
local $ENV{LANG} = "C";
@pg_lsc = `/usr/bin/pg_lsclusters`;
- (shift @pg_lsc) =~ /^Version / or die "Unexpected output from pg_lsclusters. Aborting.";
+ (shift @pg_lsc) =~ /^Ver(?:sion|) / or die "Unexpected output from pg_lsclusters. Aborting.";
}
# Inspect running instances of PostgreSQL
Modified: trunk/packages/galaxy/trunk/debian/galaxy-server-pg-database.postrm
===================================================================
--- trunk/packages/galaxy/trunk/debian/galaxy-server-pg-database.postrm 2015-02-01 13:03:34 UTC (rev 18709)
+++ trunk/packages/galaxy/trunk/debian/galaxy-server-pg-database.postrm 2015-02-01 13:04:21 UTC (rev 18710)
@@ -1,10 +1,20 @@
#!/bin/sh
set -e
+#DEBHELPER#
+
# This script used to remove lines from universe_wsgi.ini but now I'm using the modular
-# config it just restarts the server.
+# config it is simpler. I still want to rename the .ini file on removal otherwise it
+# continues to take effect.
# This script will not touch the database at all. You need to drop that yourself.
-if [ "$1" = purge -o "$1" = remove ] ; then
+if [ "$1" = purge ] ; then
+ rm -f /etc/galaxy-server/universe_wsgi.d/32_pg-database.ini.dpkg-bak
+
invoke-rc.d galaxy restart || true
+elif [ "$1" = remove ] ; then
+ ( cd /etc/galaxy-server/universe_wsgi.d && \
+ mv 32_pg-database.ini 32_pg-database.ini.dpkg-bak ) || true
+
+ invoke-rc.d galaxy restart || true
fi
Modified: trunk/packages/galaxy/trunk/debian/galaxy-server.install
===================================================================
--- trunk/packages/galaxy/trunk/debian/galaxy-server.install 2015-02-01 13:03:34 UTC (rev 18709)
+++ trunk/packages/galaxy/trunk/debian/galaxy-server.install 2015-02-01 13:04:21 UTC (rev 18710)
@@ -13,6 +13,7 @@
/usr/lib/galaxy-server/lib/
/usr/lib/galaxy-server/locale/
debian/make_transfer_dirs.sh /usr/lib/galaxy-server/
+debian/cleanup_everything.sh /usr/lib/galaxy-server/scripts/
/usr/lib/galaxy-server/manage_db.sh*
/usr/lib/galaxy-server/manage_tools.sh
/usr/lib/galaxy-server/run_demo_sequencer.sh
@@ -23,7 +24,7 @@
/usr/lib/galaxy-server/set_metadata.sh*
/usr/lib/galaxy-server/setup_rabbitmq.sh
/usr/lib/galaxy-server/tool_conf.xml.main
-/usr/lib/galaxy-server/tool-data/
+#/usr/lib/galaxy-server/tool-data
/usr/lib/galaxy-server/tool_list.py
/usr/lib/galaxy-server/tools/
/usr/share/galaxy-server/static/
@@ -39,4 +40,4 @@
/usr/lib/galaxy-server/*.xml
###Custom scripts
-debian/sbin /usr
+debian/sbin/* /usr/sbin/
Modified: trunk/packages/galaxy/trunk/debian/galaxy-server.postinst
===================================================================
--- trunk/packages/galaxy/trunk/debian/galaxy-server.postinst 2015-02-01 13:03:34 UTC (rev 18709)
+++ trunk/packages/galaxy/trunk/debian/galaxy-server.postinst 2015-02-01 13:04:21 UTC (rev 18710)
@@ -32,11 +32,17 @@
touch /usr/lib/galaxy-server/database/integrated_tool_panel.xml
#Ensure /var area is writeable
for d in /var/lib/galaxy-server/* ; do
- if [ "`basename $d`" != transfer ] ; then
+ bn="`basename $d`"
+ if [ "$bn" != transfer ] ; then
chown -R Debian-galaxy $d
chgrp Debian-galaxy $d
#but this stuff, especially the database, must not be world-readable
- chmod o-rwx $d
+ #apart from the tool-data and shed_tools folders
+ if [ "$bn" = 'tool-data' -o "$bn" = shed_tools ] ; then
+ chmod 755 $d
+ else
+ chmod 750 $d
+ fi
fi
done
Added: trunk/packages/galaxy/trunk/debian/galaxy-server.preinst
===================================================================
--- trunk/packages/galaxy/trunk/debian/galaxy-server.preinst (rev 0)
+++ trunk/packages/galaxy/trunk/debian/galaxy-server.preinst 2015-02-01 13:04:21 UTC (rev 18710)
@@ -0,0 +1,19 @@
+#!/bin/bash
+
+set -e
+set -u
+
+#DEBHELPER#
+
+# If /usr/lib/galaxy-server/tool-data is a directory and /var/lib/galaxy-server/tool-data
+# does not exist, move the thing and symlink it.
+# This reflects a layout change introduced in 20140730-0biolinux1
+
+# Ownership also needs to be changed, but this is done by postinst
+
+if [ -d /usr/lib/galaxy-server/tool-data -a ! -L /usr/lib/galaxy-server/tool-data \
+ -a -d /var/lib/galaxy-server -a ! -e /var/lib/galaxy-server/tool-data ] ; then
+ echo "Shifting tool-data into /var/lib/galaxy-server"
+ mv /usr/lib/galaxy-server/tool-data /var/lib/galaxy-server
+ ln -s /var/lib/galaxy-server/tool-data /usr/lib/galaxy-server/
+fi
Modified: trunk/packages/galaxy/trunk/debian/make_transfer_dirs.sh
===================================================================
--- trunk/packages/galaxy/trunk/debian/make_transfer_dirs.sh 2015-02-01 13:03:34 UTC (rev 18709)
+++ trunk/packages/galaxy/trunk/debian/make_transfer_dirs.sh 2015-02-01 13:04:21 UTC (rev 18710)
@@ -8,7 +8,7 @@
#If users are added to the "galaxy" group, give them a place to upload files
#directly to the server. There is a "members" command to find group members
#but I'd need to add it as a package dep and it seems a bit pointless. So...
-members(){
+members(){
g_line=`getent group "$1"`
[ -n "$g_line" ] || { echo "No such group $1." >&2 ; return 1 ; }
getent passwd | awk -F: '$4 == "'`echo "$g_line" | cut -d: -f3`'" { printf("%s ",$1) }'
@@ -26,6 +26,10 @@
/etc/galaxy-server/universe_wsgi.d/* && install -d /var/lib/galaxy-server/transfer
for m in `members galaxy` ; do
folder=/var/lib/galaxy-server/transfer/$m at localhost
- [ -e "$folder" ] && break
+ # Force permissions, because this was getting screwed up in too many cases.
+ if [ -e "$folder" ] ; then
+ chown "$m:Debian-galaxy" "$folder" && chmod 770 "$folder"
+ continue
+ fi
install -o $m -g Debian-galaxy -m 770 -d "$folder"
done
Added: trunk/packages/galaxy/trunk/debian/patches/add_favicon_to_masthead
===================================================================
--- trunk/packages/galaxy/trunk/debian/patches/add_favicon_to_masthead (rev 0)
+++ trunk/packages/galaxy/trunk/debian/patches/add_favicon_to_masthead 2015-02-01 13:04:21 UTC (rev 18710)
@@ -0,0 +1,20 @@
+--- a/templates/base/base_panels.mako
++++ b/templates/base/base_panels.mako
+@@ -299,6 +299,7 @@
+ %else:
+ <title>${self.title()}</title>
+ %endif
++ <link rel="shortcut icon" href="/galaxy/favicon.ico" type="image/x-icon" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ ## For mobile browsers, don't scale up
+ <meta name = "viewport" content = "maximum-scale=1.0">
+--- a/templates/webapps/galaxy/galaxy.panels.mako
++++ b/templates/webapps/galaxy/galaxy.panels.mako
+@@ -161,6 +161,7 @@
+ <html>
+ <head>
+ <title></title>
++ <link rel="shortcut icon" href="/galaxy/favicon.ico" type="image/x-icon" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ ## for mobile browsers, don't scale up
Added: trunk/packages/galaxy/trunk/debian/patches/commit_1298d3f
===================================================================
--- trunk/packages/galaxy/trunk/debian/patches/commit_1298d3f (rev 0)
+++ trunk/packages/galaxy/trunk/debian/patches/commit_1298d3f 2015-02-01 13:04:21 UTC (rev 18710)
@@ -0,0 +1,68 @@
+# https://bitbucket.org/galaxy/galaxy-central/commits/1298d3f
+# HG changeset patch
+# User Nate Coraor <nate at bx.psu.edu>
+# Date 1392832833 21600
+# Branch stable
+# Node ID 1298d3f6aca59825d0eb3d32afd5686c4b1b9294
+# Parent 44968207ddd283d0023c72e3d25fd39b1c71eb99
+Stop jobs when all output datasets are deleted via the API.
+
+--- a/lib/galaxy/web/base/controller.py
++++ b/lib/galaxy/web/base/controller.py
+@@ -892,6 +892,18 @@
+ break
+ return job
+
++ def stop_hda_creating_job( self, hda ):
++ """
++ Stops an HDA's creating job if all the job's other outputs are deleted.
++ """
++ if hda.parent_id is None and len( hda.creating_job_associations ) > 0:
++ # Mark associated job for deletion
++ job = hda.creating_job_associations[0].job
++ if job.state in [ self.app.model.Job.states.QUEUED, self.app.model.Job.states.RUNNING, self.app.model.Job.states.NEW ]:
++ # Are *all* of the job's other output datasets deleted?
++ if job.check_if_output_datasets_deleted():
++ job.mark_deleted( self.app.config.track_jobs_in_database )
++ self.app.job_manager.job_stop_queue.put( job.id )
+
+
+ class UsesLibraryMixin:
+--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
++++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
+@@ -278,6 +278,8 @@
+ # get_dataset can return a string during an error
+ if hda and isinstance( hda, trans.model.HistoryDatasetAssociation ):
+ changed = self.set_hda_from_dict( trans, hda, payload )
++ if payload.get( 'deleted', False ):
++ self.stop_hda_creating_job( hda )
+ except Exception, exception:
+ log.error( 'Update of history (%s), HDA (%s) failed: %s',
+ history_id, id, str( exception ), exc_info=True )
+@@ -347,6 +349,8 @@
+ trans.sa_session.flush()
+ rval[ 'purged' ] = True
+
++ self.stop_hda_creating_job( hda )
++
+ trans.sa_session.flush()
+ rval[ 'deleted' ] = True
+
+--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
++++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
+@@ -839,14 +839,7 @@
+ hda.mark_deleted()
+ hda.clear_associated_files()
+ trans.log_event( "Dataset id %s marked as deleted" % str(id) )
+- if hda.parent_id is None and len( hda.creating_job_associations ) > 0:
+- # Mark associated job for deletion
+- job = hda.creating_job_associations[0].job
+- if job.state in [ self.app.model.Job.states.QUEUED, self.app.model.Job.states.RUNNING, self.app.model.Job.states.NEW ]:
+- # Are *all* of the job's other output datasets deleted?
+- if job.check_if_output_datasets_deleted():
+- job.mark_deleted( self.app.config.track_jobs_in_database )
+- self.app.job_manager.job_stop_queue.put( job.id )
++ self.stop_hda_creating_job( hda )
+ trans.sa_session.flush()
+ except Exception, e:
+ msg = 'HDA deletion failed (encoded: %s, decoded: %s)' % ( dataset_id, id )
Added: trunk/packages/galaxy/trunk/debian/patches/fix_build_universe_config
===================================================================
--- trunk/packages/galaxy/trunk/debian/patches/fix_build_universe_config (rev 0)
+++ trunk/packages/galaxy/trunk/debian/patches/fix_build_universe_config 2015-02-01 13:04:21 UTC (rev 18710)
@@ -0,0 +1,11 @@
+--- a/scripts/build_universe_config.py
++++ b/scripts/build_universe_config.py
+@@ -11,7 +11,7 @@
+ message = "%s: Must specify directory to merge configuration files from." % argv[0]
+ raise Exception(message)
+ conf_directory = argv[1]
+- conf_files = [f for f in listdir(conf_directory) if match(r'.*\.ini', f)]
++ conf_files = [f for f in listdir(conf_directory) if match(r'.*\.ini$', f)]
+ conf_files.sort()
+
+ parser = ConfigParser()
Added: trunk/packages/galaxy/trunk/debian/patches/fix_workflow_misconfiguration_report
===================================================================
--- trunk/packages/galaxy/trunk/debian/patches/fix_workflow_misconfiguration_report (rev 0)
+++ trunk/packages/galaxy/trunk/debian/patches/fix_workflow_misconfiguration_report 2015-02-01 13:04:21 UTC (rev 18710)
@@ -0,0 +1,16 @@
+# This patch addresses http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010303.html
+--- a/templates/webapps/galaxy/workflow/run.mako
++++ b/templates/webapps/galaxy/workflow/run.mako
+@@ -582,9 +582,12 @@
+ # Filter possible inputs to data types that are valid for subsequent steps
+ type_filter = []
+ for oc in step.output_connections:
++ try:
+ for ic in oc.input_step.module.get_data_inputs():
+ if 'extensions' in ic and ic['name'] == oc.input_name:
+ type_filter += ic['extensions']
++ except AttributeError:
++ pass
+ if not type_filter:
+ type_filter = ['data']
+ %>
Modified: trunk/packages/galaxy/trunk/debian/patches/relax_password_length_restriction
===================================================================
--- trunk/packages/galaxy/trunk/debian/patches/relax_password_length_restriction 2015-02-01 13:03:34 UTC (rev 18709)
+++ trunk/packages/galaxy/trunk/debian/patches/relax_password_length_restriction 2015-02-01 13:04:21 UTC (rev 18710)
@@ -13,9 +13,9 @@
+VALID_EMAIL_RE = re.compile( "[^@]+@[^@]+" )
FILL_CHAR = '-'
- def validate_email( trans, email, user=None, check_dup=True ):
+
@@ -32,12 +33,8 @@
- return ''
+ # letters, numbers, and the '-' character.
if user and user.username == publicname:
return ''
- if trans.webapp.name == 'tool_shed':
@@ -29,9 +29,9 @@
if len( publicname ) > 255:
return "Public name cannot be more than 255 characters in length"
if not( VALID_PUBLICNAME_RE.match( publicname ) ):
-@@ -61,8 +58,8 @@
- return ''
+@@ -63,8 +60,8 @@
+
def validate_password( trans, password, confirm ):
- if len( password ) < 6:
- return "Use a password of at least 6 characters"
@@ -39,12 +39,10 @@
+ return "Use a password of at least 3 characters"
elif password != confirm:
return "Passwords do not match"
-- return ''
-\ No newline at end of file
-+ return ''
+ return ''
--- a/lib/galaxy/web/base/controllers/admin.py
+++ b/lib/galaxy/web/base/controllers/admin.py
-@@ -720,8 +720,8 @@
+@@ -722,8 +722,8 @@
user = get_user( trans, user_id )
password = kwd.get( 'password', None )
confirm = kwd.get( 'confirm' , None )
Modified: trunk/packages/galaxy/trunk/debian/patches/series
===================================================================
--- trunk/packages/galaxy/trunk/debian/patches/series 2015-02-01 13:03:34 UTC (rev 18709)
+++ trunk/packages/galaxy/trunk/debian/patches/series 2015-02-01 13:04:21 UTC (rev 18710)
@@ -6,3 +6,6 @@
force_use_of_bash_interpreter
drop_tmp_table_before_upgrade
shed_tools_data_path
+fix_build_universe_config
+add_favicon_to_masthead
+fix_workflow_misconfiguration_report
Modified: trunk/packages/galaxy/trunk/debian/patches/shed_tools_data_path
===================================================================
--- trunk/packages/galaxy/trunk/debian/patches/shed_tools_data_path 2015-02-01 13:03:34 UTC (rev 18709)
+++ trunk/packages/galaxy/trunk/debian/patches/shed_tools_data_path 2015-02-01 13:04:21 UTC (rev 18710)
@@ -1,8 +1,8 @@
--- a/lib/tool_shed/util/tool_util.py
+++ b/lib/tool_shed/util/tool_util.py
-@@ -207,7 +207,7 @@
- def copy_sample_file( app, filename, dest_path=None ):
- """Copy xxx.sample to dest_path/xxx.sample and dest_path/xxx. The default value for dest_path is ~/tool-data."""
+@@ -212,7 +212,7 @@
+ is ~/tool-data.
+ """
if dest_path is None:
- dest_path = os.path.abspath( app.config.tool_data_path )
+ dest_path = os.path.abspath( app.config.shed_tool_data_path )
Modified: trunk/packages/galaxy/trunk/debian/patches/tell_user_how_to_add_administrator
===================================================================
--- trunk/packages/galaxy/trunk/debian/patches/tell_user_how_to_add_administrator 2015-02-01 13:03:34 UTC (rev 18709)
+++ trunk/packages/galaxy/trunk/debian/patches/tell_user_how_to_add_administrator 2015-02-01 13:04:21 UTC (rev 18710)
@@ -1,8 +1,8 @@
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
-@@ -767,6 +767,9 @@
+@@ -782,6 +782,9 @@
success = False
- else: # User activation is OFF, proceed without sending the activation email.
+ else: # User activation is OFF, proceed without sending the activation email.
message = 'Now logged in as %s.<br><a target="_top" href="%s">Return to the home page.</a>' % ( user.email, url_for( '/' ) )
+
+ message += '''<br><br><i>If you want this user to be an administrator in Galaxy, you need to run the command </i>
Modified: trunk/packages/galaxy/trunk/debian/patches/use_system_python_libs
===================================================================
--- trunk/packages/galaxy/trunk/debian/patches/use_system_python_libs 2015-02-01 13:03:34 UTC (rev 18709)
+++ trunk/packages/galaxy/trunk/debian/patches/use_system_python_libs 2015-02-01 13:04:21 UTC (rev 18710)
@@ -2,7 +2,7 @@
+++ b/eggs.ini
@@ -11,6 +11,11 @@
; these eggs must be scrambled for your local environment
- no_auto = pbs_python DRMAA_python
+ no_auto = pbs_python
+; A version of "LOCAL" means use whatever is on the system.
+; It is assumed that these are tracked by an external package manager (eg. Dpkg)
@@ -10,9 +10,9 @@
+; Local psycopg2 is needed, I think, or else connection fails.
+
[eggs:platform]
- bx_python = 0.7.1
+ bx_python = 0.7.2
Cheetah = 2.2.2
-@@ -21,8 +26,8 @@
+@@ -20,8 +25,8 @@
PyRods = 3.2.4
numpy = 1.6.0
pbs_python = 4.3.5
Modified: trunk/packages/galaxy/trunk/debian/rules
===================================================================
--- trunk/packages/galaxy/trunk/debian/rules 2015-02-01 13:03:34 UTC (rev 18709)
+++ trunk/packages/galaxy/trunk/debian/rules 2015-02-01 13:04:21 UTC (rev 18710)
@@ -15,6 +15,9 @@
%:
dh $@ --with python2
+override_dh_builddeb:
+ dh_builddeb -- -Z xz
+
override_dh_auto_clean:
#Man there is a lot of crud in here...
dh_auto_clean
@@ -29,9 +32,13 @@
rm -rf database/tmp
rm -f lib/galaxy/datatypes/test/temp.txt
#./debian/remove_obsolete_eggs.sh
+ rm -rf static/scripts/packed
override_dh_auto_build:
chmod a-x tool-data/*.loc.sample
+ #Note pack_scripts.py needs Java, but doesn't throw an error if java is missing
+ which java
+ cd static/scripts && ./pack_scripts.py
# Custom manual install to debian/tmp. Sorry - long winded.
override_dh_auto_install:
@@ -44,11 +51,12 @@
mkdir -p debian/tmp/var/lib/galaxy-server/genetrack_plots
cp -r * debian/tmp/usr/lib/galaxy-server || true
( cd ./debian/tmp ; ../copy_sample_config.sh )
- mv debian/tmp/usr/lib/galaxy-server/database debian/tmp/var/lib/galaxy-server
- mv debian/tmp/usr/lib/galaxy-server/static debian/tmp/usr/share/galaxy-server
- mv debian/tmp/usr/lib/galaxy-server/templates debian/tmp/usr/share/galaxy-server
- mv debian/tmp/usr/lib/galaxy-server/test debian/tmp/usr/share/galaxy-server
- mv debian/tmp/usr/lib/galaxy-server/test-data debian/tmp/usr/share/galaxy-server
+ for x in tool-data database ; do \
+ mv debian/tmp/usr/lib/galaxy-server/$$x debian/tmp/var/lib/galaxy-server ; \
+ done
+ for x in static templates test test-data ; do \
+ mv debian/tmp/usr/lib/galaxy-server/$$x debian/tmp/usr/share/galaxy-server ; \
+ done
mv debian/tmp/usr/lib/galaxy-server/eggs/*.egg-tmp debian/tmp/var/lib/galaxy-server/egg-cache || true
find debian/tmp/usr/share -type f -exec chmod a-x '{}' ';'
chmod a+x debian/tmp/usr/lib/galaxy-server/*.sh
@@ -67,8 +75,9 @@
find debian/tmp/usr -name '*.py' -exec sed -i -e '1s/#! \?.*python[0-9.]*/#!\/usr\/bin\/python/' '{}' \;
override_dh_install:
- dh_install
+ dh_install -X.svn
#Make a load of symlinks to allow Galaxy to write to various directories, but only in /var/lib/galaxy-server
+ dh_link -pgalaxy-server /var/lib/galaxy-server/tool-data /usr/lib/galaxy-server/tool-data
dh_link -pgalaxy-server /var/lib/galaxy-server/database /usr/lib/galaxy-server/database
dh_link -pgalaxy-server /var/lib/galaxy-server/shed_tools /usr/lib/galaxy-server/shed_tools
dh_link -pgalaxy-server /usr/share/galaxy-server/static /usr/lib/galaxy-server/static
Modified: trunk/packages/galaxy/trunk/debian/run.sh
===================================================================
--- trunk/packages/galaxy/trunk/debian/run.sh 2015-02-01 13:03:34 UTC (rev 18709)
+++ trunk/packages/galaxy/trunk/debian/run.sh 2015-02-01 13:04:21 UTC (rev 18710)
@@ -9,6 +9,9 @@
#Galaxy does expect somewhere to unpack 'eggs'
export PYTHON_EGG_CACHE=/var/lib/galaxy-server/egg-cache
+# Needed to make gops_join work...
+export PYTHONPATH=`echo /usr/lib/galaxy-server/eggs/bx_python-*.egg | tr ' ' ':'`
+
#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"`
@@ -35,9 +38,10 @@
# unless you are are doing it for testing purposes.
UWINI=universe_wsgi.ini
-if [ ! -e $UWINI ] ; then
+if [ ! -e "$UWINI" ] ; then
UWINI=`mktemp --tmpdir universe_wsgi_XXXX.ini`
python ./scripts/build_universe_config.py universe_wsgi.d/ "$UWINI"
+ chmod g+r "$UWINI"
fi
#For some reason I seem to be having issues initialising the database when it's
Modified: trunk/packages/galaxy/trunk/debian/universe_wsgi.d/31_apache-proxy.ini
===================================================================
--- trunk/packages/galaxy/trunk/debian/universe_wsgi.d/31_apache-proxy.ini 2015-02-01 13:03:34 UTC (rev 18709)
+++ trunk/packages/galaxy/trunk/debian/universe_wsgi.d/31_apache-proxy.ini 2015-02-01 13:04:21 UTC (rev 18710)
@@ -14,4 +14,4 @@
# There is no neat way to log out a user with Basic Auth, but here is a non-neat way.
# Not yet tested on IE.
-remote_user_logout_href = javascript:var r=new XMLHttpRequest();r.onreadystatechange=function(){if(r.readyState==4)window.location.replace('logout.html')};r.open('get','logout.html',true,'logout','logout');r.send();
+remote_user_logout_href = logout1.html
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