Nicola Soranzo
7866f2dcfd
Merge rolling_restart.sh in run.sh by adding --wait parameter.
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Also add the following combination:
GALAXY_RUN_ALL=1 ./run.sh --daemon --wait
which, by preventing servers from starting simultaneously, is useful when
multiple servers are configured before creating the database, or when updating
to a new Galaxy release containing a database upgrade.
2015-02-02 16:08:13 +00:00
Nicola Soranzo
4c5c75ee4b
Allow "GALAXY_RUN_ALL=1 ./run.sh restart" since --daemon is implied.
2015-02-02 15:46:48 +00:00
Dave Bouvier
05cdaadfb9
Allow a Galaxy admin to configure environment variables (e.g. $PATH) for their local Galaxy installation without altering the environment for their shell.
2015-01-28 11:50:31 -05:00
Dannon Baker
504d3b6ba2
Log when using virtualenv at Galaxy startup.
2015-01-26 08:54:29 -05:00
Nate Coraor
b376ed7664
Fix a bug with config/galaxy.ini in run.sh
2014-09-16 17:13:17 -04:00
Nate Coraor
267e4d9b88
Don't create galaxy.ini, just use the sample if galaxy.ini does not exist. Also fix startup when galaxy.ini.sample. Fixes the universe_wsgi.ini skipping problem Dannon found.
2014-09-15 22:12:18 -04:00
Nate Coraor
8fadc6392b
Rename universe_wsgi.ini -> galaxy.ini everywhere.
2014-09-15 16:43:51 -04:00
Lance Parsons
29d56e518d
Source virtualenv before python check and for reports app
2014-09-04 15:12:04 -04:00
Nate Coraor
4d79575ed2
Automatically use a virtualenv in galaxy_root/.venv/ if it exists (a la Pulsar).
2014-07-11 09:58:08 -04:00
Dave Bouvier
8b45411adf
Abstract common startup tasks into scripts/common_startup.sh, which used to be copy_sample_files.sh.
2014-06-13 16:39:59 -04:00
Dave Bouvier
4f2e506042
Enable running the create_users and create_categories scripts via run_tool_shed.sh
2014-05-22 10:59:18 -04:00
John Chilton
efdafb2f68
Enable job metrics by default.
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They should work with all stock Galaxy runners now.
2014-05-20 15:31:14 -05:00
Nate Coraor
794484e8c3
Rename ucsc_build_sites.txt to .sample.
2014-02-27 16:37:48 -05:00
Daniel Blankenberg
1c9861eca2
First pass at a plugable Data Manager. Data Managers can be defined locally or installed from a Tool Shed. TODO: Display Data Manager information in the Tool Shed. Do not install Data Managers into Tool Panel. Add tests. Write Docs.
2013-02-14 15:13:06 -05:00
Greg Von Kuster
a2e5b2fe77
Maintain entries for Galaxy's ToolDataTableManager acquired from installed tool shed repositrories that contain a valid file named tool_data_table_conf.xmnl.sample in a separate config file name shed_tool_data_table_conf.xml. This will ensure that manual edits to the original tool_data_table_conf.xml will not be munged when Galaxy's tool shed installation process automatically adds entries into the file. This enhancement alos includes a bug fix where ToolDataTableEntries that should have been persisted to the XML file were not being handled correctly.
2012-11-07 16:36:28 -05:00
Nate Coraor
5752c297d9
Merged in jmchilton/galaxy-central-configuration-directory (pull request #44 )
2012-08-15 10:57:14 -04:00
Dave Bouvier
36dbacf8f1
Cleaned up code, added searchable list of NCBI builds.
2012-07-05 09:56:54 -04:00
Scott McManus
6f589136da
Added application of regular expressions and exit code. Pulling exit
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codes from the runners will be part of a separate submission.
2012-06-19 11:35:36 -04:00
John Chilton
7ba16d90ad
Augment run.sh to search for the optional environment variable
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GALAXY_UNIVERSE_CONFIG_DIR. If this is set, before Galaxy is launched
the directory specified by the environment variable is searched for
ini config files. These files are merged into a single configuration
structure and written back out as universe.ini.
This should allow for a more modular configuration of Galaxy. The
files are merged in lexiographic order and later files can override
properties specified ealier on. If a consistent naming scheme is used
this can be really useful:
As an example, one might specify the files as such:
000_galaxy_defaults.ini
000_default_sqlite_config.ini
100_institution_specific.ini
500_job_runner.ini
500_webapp_0.ini
500_webapp_1.ini
500_instance_specific.ini
500_available_postgres.ini
2012-05-04 00:12:43 -05:00
Nate Coraor
0a0a5a4b74
Allow for starting/stopping multiple servers directly in run.sh.
2012-04-16 16:26:10 -04:00
Daniel Blankenberg
eed27b829a
Abstract OpenID providers to be defined outside of the Python code and to allow customization of actions. See individual examples in openid/ and the list of enabled OpenID providers in openid_conf.xml.sample. Feedback is welcomed.
2012-03-23 13:41:01 -04:00
Greg Von Kuster
e0942033ba
The InstallManager is now a stand-alone appication that attempts to load the tool panel as closely as possible to the way it was loaded before tools were migrated from the Galaxy distribution to the tool shed.
2012-02-28 11:38:08 -05:00
Daniel Blankenberg
aa5eb3c4a4
Add tool-data/shared/rviewer/rviewer_build_sites.txt.sample to run.sh sample list.
2012-02-17 10:04:28 -05:00
Daniel Blankenberg
09bcf6e95a
Add VCF viewer for IGV. Add necessary datatypes and converters to support this view (vcf_bgzip; vcf_bgzip to tabix).
2011-11-15 17:24:38 -05:00
Greg Von Kuster
516a5f3874
Add new sample config to point to tools installed from a tool shed and add additional directories for checking/creating at startup.
2011-09-06 13:41:06 -04:00
Nate Coraor
758e13ac28
Remove hardcoding of universe_wsgi.ini, fixes issue #358 (except for the sample cleanup scripts which, as samples, are expected to be modified by the site anyway).
2011-06-08 12:10:51 -04:00
Daniel Blankenberg
0c08b00f70
Add external_service_types_conf.xml.sample to list of configuration files that need to be initialized by setup.sh and run.sh.
2011-01-11 09:40:42 -05:00
Nate Coraor
3fb1a2d715
Move static/welcome.html to a sample file which will be copied to the actual welcome.html upon first run.
2010-11-30 14:07:08 -05:00
Nate Coraor
d0f5f965fa
Automatically find new .sample files in tool-data/.
2010-11-05 15:13:06 -04:00
Nate Coraor
bc3490e9e8
Remove the need for setup.sh - All configuration is done in run.sh/galaxy.config.
2010-11-05 14:55:02 -04:00
Nate Coraor
2bd25bf652
Remove builds.txt from source control - use builds.txt.sample instead and copy it over if you don't have one
2010-05-10 12:50:09 -04:00
Nate Coraor
006716f53a
Egg support overhaul, introduces a number of fixes to the ABI recognition, better build scripts, a rewrite of the eggs library and eliminition of the need for python -ES
2010-03-01 15:41:30 -05:00
Nate Coraor
1f5e079a3a
python run from virtualenv sets up site.py to pull things from the real python's lib directory, so 'python -S' breaks it. To fix this, have the check_python.py script check for virtualenv and output the arguments that should be used to start python ('python -E' for virtualenv, 'python -ES' for real), then use these arguments anywhere 'python -ES' was used in the past.
2010-01-04 12:51:34 -05:00
Nate Coraor
a3d62f4036
Explicitly check eggs and fetch when starting, instead of relying on automatic in-process fetching. Also contains a fix for pysqlite egg building
2009-11-16 14:42:09 -05:00
Ian Schenck
985f7c63fa
Collapsed changeset: Trackster plugged into galaxy with behind-the-scenes indexing of Wiggle, coverage and interval datasets.
2009-03-11 00:29:01 +00:00
Nate Coraor
7560751dc8
Separate framework and tool environments.
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Whether running locally or via PBS, $PATH should now be handled in your
user's environment.
This also fixes problems like PYTHONPATH on the new blast nodes being
wrong (because they are x86_64 and the frontends are i686).
Note that you can actually start Galaxy without having an eggs dir now.
2008-04-11 20:11:21 +00:00
Nate Coraor
5f189e45c3
The enormous eggs-out-of-svn commit. More details at:
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http://g2.trac.bx.psu.edu/wiki/GalaxyEggs
2008-03-27 19:27:05 +00:00
James Taylor
a50b8007ef
Splitting out UCS2 and UCS4 eggs for linux. Run scripts check
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waht python is available and use the right directory. Factored
path stuff out of shell scripts into a shared 'setup_paths.sh'.
2007-12-06 01:27:33 +00:00
Nate Coraor
61748c469b
make run.sh bourne-friendly.
2007-10-19 14:42:31 +00:00
Nate Coraor
4d720d63c6
Removed tmp and files from svn, now automatically created via run.sh
2007-05-02 19:23:00 +00:00
Nate Coraor
092c23f41b
Made run.sh Bourne-friendly and added path fix for cluster nodes.
2007-02-16 21:21:24 +00:00
Daniel Blankenberg
547ecf0960
Removing arch and module directories. Removing old operations (and tests), since they require arch; updated tool_conf.xml.sample.
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Removed non-arch specific cheetah egg, since compiled c code (once located in arch) is included in arch specific eggs. Removed a
tool called basicStats2, which used arch, but hasn't been in tool_conf.xml for some time.
2007-01-16 17:05:33 +00:00
James Taylor
2c4c20436e
Cleaning up modules. Still a few stragglers that can't be easily eggified.
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EVERYTHING we depend on should eventually be under the galaxy module or
packaged in eggs to avoid namespace problems.
2006-11-15 18:27:21 +00:00
James Taylor
d87ee75027
Cleaning everything up (should be working as usual)
2006-11-15 16:55:17 +00:00
James Taylor
f788a34fca
Moving james-wsgi branch to new trunk.
2006-11-15 16:28:21 +00:00
Nicola Soranzo