James Taylor
15ec130bfb
core: add PasteDeploy dependency back, used inside Paste#httpserver
2013-02-01 17:30:58 -05:00
James Taylor
f6629fd8c4
changeset: 8701:c3ac9849dd1b
...
branch: unstable
tag: tip
user: James Taylor <james@jamestaylor.org >
summary: core: pull the pieces of PasteScript we use into galaxy.util.pastescript. Remove all dependencies on PasteScript and PasteDeploy. Begin stripping down the serve command so we can start to enhance it for our needs.
2013-01-30 15:26:00 -05:00
Carl Eberhard
fdbf75864f
Enable serving static files when running functional tests
2013-01-17 14:58:43 -05:00
Greg Von Kuster
1c7ef874b5
Utility code cleanup and import tweaking.
2012-12-13 11:41:31 -05:00
Carl Eberhard
b6d4e00bc2
Fixes to history functional tests; Twilltestcase: added function to parse and check json, exact string matcher
2012-12-10 17:44:11 -05:00
Greg Von Kuster
c48f54ee3c
Merged in lance_parsons/galaxy-central_installed-tools-functional-tests-fix (pull request #95 )
2012-12-07 19:09:00 -05:00
Lance Parsons
0e7a2b7324
Fix for finding test-data for installed tools
...
See bug: https://trello.com/c/Z0vhJEq6
2012-12-07 17:22:48 -05:00
Dave Bouvier
de7cb21382
Migrate tools to tool shed: addValue, ChangeCase, Condense characters1, Convert characters1, Cut1, mergeCols1, Remove beginning1, Show beginning1, Show tail1, trimmer
2012-12-07 16:08:40 -05:00
Kyle Ellrott
53e4dc4f6b
Patch to make extended_metadata loader work better, and fixing library loader to catch non-ascii errors
2012-11-30 10:58:39 -08:00
Dave Bouvier
917d5a72e8
Migrated lastz and bowtie tools to the tool shed. Added a target_file feature to the tool dependency installation process.
2012-11-26 10:18:47 -05:00
Dannon Baker
e660fb2591
Merged in jmchilton/galaxy-central-reports-config-enhancements (pull request #71 )
2012-11-12 12:00:18 -05:00
Dannon Baker
e4b98ca9b5
Merged in kellrott/galaxy-central (pull request #81 )
2012-11-12 11:54:45 -05:00
Dave Bouvier
576ceb7829
Revert tool migration.
2012-12-07 16:38:26 -05:00
Greg Von Kuster
ed060ddcbe
Add the shed_tool_data_table_config to the functional test's app.
2012-11-08 11:41:21 -05:00
Greg Von Kuster
d0438ecb2f
Since tool migration scripts can be executed any number of times, make sure that no repositories are installed if not tools associated with the migration are defined in the tool_conf.xml file (or equivalent). This fix is associated only with the recently introduced Galaxy admin UI feature displaying the list of migration stages currently available. This is the way the migration process at server startup has always worked so no changes are needed in that scenario.
2012-11-07 10:51:35 -05:00
Daniel Blankenberg
e316254e28
Change indent from 3 spaces to 4 for 8171:4b62ed46e5b6.
2012-11-07 10:45:10 -05:00
Daniel Blankenberg
bbeed4dc0b
Use check_python() to verify python version in set_metadata.py instead of hardcoded minimum version check.
2012-11-07 10:35:56 -05:00
Kyle Ellrott
4e8d938ff7
Adding the initial componenents of an extended metadata system for datasets.
...
The idea behind an 'extended metadata' for datasets is to provide a mechanism to encode
and index user generated metadata and keep it attached to files. Users can provide a
JSON style data structure which will then be indexed and stored. Later this index can
be used to search and discover datasets via a pseudo-formal schema.
This patch introduces the tables, and makes it possible to inject user metadata into a file
load using the 'extended_metadata' field in the query.
2012-10-28 00:28:42 -07:00
Dave Bouvier
cc608c31b2
Updated migration script to reference repository with correct use of tool dependency tag sets.
2012-10-25 13:25:39 -04:00
Dave Bouvier
c968460662
Migrate Picard tools to the tool shed.
2012-10-24 11:09:20 -04:00
Scott McManus
a0afee842e
Re-commit new /api/folders section
2012-10-15 18:09:25 -04:00
Scott McManus
0148eabc72
Backout
2012-10-15 17:53:37 -04:00
Scott McManus
954e96fc34
Added /api/folders. The api_folders configuration variable controls access to it (and is False by default).
2012-10-15 17:29:29 -04:00
Daniel Blankenberg
94a2f94529
Fix minor typos in db_shell.py
2012-10-11 16:43:37 -04:00
Nate Coraor
9213c344db
Fix reporting in the set_user_disk_usage.py script.
2012-10-03 13:40:54 -04:00
Nate Coraor
9ab95a9fa9
Fix passing of job name when running jobs as a system user.
2012-10-03 11:51:07 -04:00
Nate Coraor
1e2256fe0e
pgcleanup: Print a useful message if no options are given.
2012-10-01 13:45:37 -04:00
Nate Coraor
8193489dda
pgcleanup/set_user_disk_usage: set usage to 0, not null, when the user has no active data.
2012-09-28 16:11:38 -04:00
Dave Bouvier
c2eeee7b9f
Migrate BWA to the tool shed.
2012-09-28 15:35:44 -04:00
Nate Coraor
caa06bbc20
Allow Postgres users to update user disk usage with a fast wCTE rather than a slower computation in Python.
2012-09-28 14:30:10 -04:00
John Chilton
c3e99bc384
Improvements to reports management script (run_reports.sh) to enable managing the reports app from CloudMan. These enhancements are all "optional", the default behavior of run_reports.sh is unchanged.
...
Added flag (--sync-config) to run_reports.sh script that will cause it to synchronize the database connection and file path properties in reports_wsgi.ini with those in universe_wsgi.ini prior to starting paster app.
Allow specification of reports configuration directory mirroring similar extensions previously accepted for universe config and run.sh
Added usage documentation to run_reports.sh.
Added extension points to tweak pid and log location for reports application via environment variables.
2012-09-21 22:04:15 -05:00
Dannon Baker
ba6114ca3e
Fix create_all_fasta_loc to work when inspect_dir is not set.
2012-09-18 20:49:29 -04:00
Nate Coraor
459d3a2c1d
More pgcleanup.py fixes and addition of cleanup event tables for library items.
2012-09-17 12:51:17 -04:00
Nate Coraor
71d7f7c132
Distributed object store fixes for pgcleanup.py.
2012-09-11 12:22:03 -04:00
Nate Coraor
0e1b041cde
Bug fixes for pgcleanup.py
2012-09-10 16:59:33 -04:00
Nate Coraor
c8e49cdd6d
Bugfix for pgcleanup.py
2012-09-10 14:07:05 -04:00
Nate Coraor
e19092e9c5
Add a dataset cleanup script that's optimized for (and compatible only with) PostgreSQL 9.1+. Also add a bunch of tables for logging all cleanup events, which makes reversing such events trivial.
2012-09-10 12:03:23 -04:00
Richard Park
6839829211
Cleaned up codebase for attempting adding api additions to the galaxy main branch
2012-08-03 02:09:05 -04:00
Richard Park
e6d5c55c89
Updated notes on how to run api/workflow_execute_parameters.py
2012-04-10 23:00:41 -04:00
Richard Park
412f779f76
Updated scripts for API workflow enhancements and changing workflow parameters programatically
2012-02-01 16:21:38 -05:00
Dannon Baker
3d5fd7b5e2
Migrate NCBI Blast+ (and blastxml) to the toolshed.
2012-08-17 11:35:31 -04:00
Nate Coraor
5752c297d9
Merged in jmchilton/galaxy-central-configuration-directory (pull request #44 )
2012-08-15 10:57:14 -04:00
Nate Coraor
a7f4a7534a
Merged in jmchilton/galaxy-central-preseeding (pull request #38 )
2012-08-15 10:54:50 -04:00
Carl Eberhard
d97ada4bb5
minor docstring adds in /scripts
2012-08-03 13:31:48 -04:00
Greg Von Kuster
7992dfa449
Another change to installed changed revision for the freebayes tool migration process.
2012-07-13 12:53:42 -04:00
Greg Von Kuster
2c87a63983
Change ethe installed changed revision for the freebayes tool migration process.
2012-07-13 12:50:29 -04:00
Greg Von Kuster
5c8fe01456
Migrate the freebayes tool out of the Galaxy code distribution.
2012-07-10 16:23:34 -04:00
Enis Afgan
fa1959b579
Fix API history purge; a few documentation corrections
2012-06-18 14:53:02 +10:00
John Chilton
55b451dcf4
Fix a typo.
2012-05-24 07:47:14 -05:00
John Chilton
7ba16d90ad
Augment run.sh to search for the optional environment variable
...
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
James Taylor