John Chilton
f05eacf362
Functional tool test fix.
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No tests with a repeat and min=1 were ever going to past.
2013-11-17 02:03:28 -06:00
John Chilton
4cba87cc16
PEP-8 and style adjustments for lib/galaxy/webapps/galaxy/api/provenance.py.
2013-11-17 00:53:00 -06:00
John Chilton
ddab3d2239
Consolidate duplicated code for loading HDAs from the API.
2013-11-17 00:47:26 -06:00
John Chilton
fcaa566e60
Fix logic in tool's populate_state logic to handle multiple uploads.
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Enables composite uploads through API.
2013-11-17 00:47:26 -06:00
John Chilton
6ef8fc7181
Do not reference values before use when GALAXY_TEST_EXTERNAL used.
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GALAXY_TEST_EXTERNAL still quite broken.
2013-11-17 00:47:26 -06:00
Nate Coraor
c014405099
Merged in nsoranzo/galaxy-central (pull request #262 )
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Convert other 3 tools to $GALAXY_SLOTS
2013-11-15 19:05:06 -05:00
Nicola Soranzo
3e528ae02b
Enhance bowtie2 to utilize GALAXY_SLOTS configuration when available.
2013-11-16 00:53:52 +01:00
Nicola Soranzo
c4e9999a33
Enhance mosaik to utilize GALAXY_SLOTS configuration when available.
2013-11-16 00:53:35 +01:00
Nicola Soranzo
a481327ab3
Enhance trinity to utilize GALAXY_SLOTS configuration when available.
2013-11-16 00:52:36 +01:00
Carl Eberhard
dd315841b2
History panel: fix disabled class on icon buttons
2013-11-15 15:53:59 -05:00
Carl Eberhard
d06f88455e
Update jquery.form.js to 3.45 and fix chrome upload bug; pack scripts
2013-11-15 15:18:18 -05:00
Nate Coraor
3f11b97087
Merge stable.
2013-11-15 14:19:09 -05:00
Nate Coraor
ce31bc4742
Properly handle PBS' -q argument.
2013-11-15 14:18:09 -05:00
Nate Coraor
b9b735a7f7
Detect nginx upload injected params in the API tool runner.
2013-11-15 14:15:00 -05:00
Dave Bouvier
44d7f92352
Fix for exporting a repository with a complex repository dependency.
2013-11-15 11:14:26 -05:00
Dave Bouvier
92998fb377
Fix for exporting a repository capsule.
2013-11-15 10:50:49 -05:00
John Chilton
3fe4ea3d52
Merge latest stable.
2013-11-15 08:20:36 -06:00
John Chilton
553efe99d3
Fix small typo in 9ce5afd (tool shed autoconf action).
2013-11-15 08:20:06 -06:00
John Chilton
7f9712c48c
Fix bug in 4f7e715 that actually allows multiple repeat values to be specified via API.
2013-11-14 23:39:52 -06:00
John Chilton
3d03f12e0a
PEP-8 fixes for test/base/twilltestcase.py.
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Still hundreds of lines to fix.
2013-11-14 17:49:58 -06:00
Dave Bouvier
249082d983
Remove reference to undefined variable.
2013-11-14 18:43:58 -05:00
Dave Bouvier
261d60656a
Remove a return that was added while debugging.
2013-11-14 17:50:54 -05:00
Dave Bouvier
84a3848150
Fix broken import.
2013-11-14 17:37:27 -05:00
Dave Bouvier
4802b75a26
Correct wrong method call.
2013-11-14 17:00:11 -05:00
Dave Bouvier
910c84ed99
Substantial refactoring of the install and test framework to address a number of weaknesses.
2013-11-14 16:52:06 -05:00
Dave Bouvier
4570330e25
Rebuild the list of sniffer elem classes after each one is removed from sniffer_elems, in order to keep the mapping current.
2013-11-14 16:31:34 -05:00
Greg Von Kuster
81a793973d
Display an error message rather than raising an exception when handling invalid complex repository dependencies in the Tool Shed.
2013-11-14 15:51:24 -05:00
John Chilton
ed9a868424
get_intiail_value history fix. Allows ToolDataParameters inside of repeats when using API.
2013-11-14 12:35:27 -06:00
John Chilton
a99b8dabd1
Merged in jmchilton/galaxy-central-fork-1 (pull request #256 )
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API Enhancements Required for API Driven Tool Testing
2013-11-14 12:34:05 -06:00
John Chilton
ada56ff926
Clean up 4f7e715 slightly.
2013-11-14 12:32:24 -06:00
John Chilton
f55fa932b2
Outline some enhancements to InstallEnvironment, not used yet.
2013-11-14 10:39:49 -06:00
John Chilton
3ac40f6d36
Bring in action fix from @BjoernGruening, not included in previous commit.
2013-11-14 10:39:49 -06:00
John Chilton
74fc1467a4
Pull in dependant R, Ruby, and Perl complete environments at recursively runtime.
2013-11-14 10:39:49 -06:00
John Chilton
ece0be9865
Introduce higher level abstraction for building up env.sh files in fabric_util.py.
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Use it to reduced duplicated code in fabric_util.py. Implement unit tests describing this new class.
2013-11-14 10:39:49 -06:00
John Chilton
716d66564e
Add new action to create_or_update_env_shell_file for sourcing other env.sh files.
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With unit test.
2013-11-14 10:39:49 -06:00
John Chilton
2c1c4c1472
Add unit test for all existing functionality in td_common_util.create_or_update_env_shell_file
2013-11-14 10:39:49 -06:00
John Chilton
640a16a86a
Update perl to use parse_setup_environment_repositories.
2013-11-14 10:39:49 -06:00
John Chilton
96487576b7
Introduce utility method parse_setup_environment_repositories.
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Use to reduce code duplication in install_util and provides target for unit tests of new functionality. Add unit tests. Add new functionality for parsing out which packages should be recursive runtime dependencies (not implemented on fabric side yet).
2013-11-14 10:39:49 -06:00
Bjoern Gruening
4fc3562c04
fix c&p leftovers in comments
2013-11-14 10:39:49 -06:00
Bjoern Gruening
2168e50668
add setup_perl_environment as Tool Shed functionality
2013-11-14 10:39:49 -06:00
Jeremy Goecks
34535d0f8e
Merge stable with default branch.
2013-11-14 11:00:58 -05:00
Jeremy Goecks
dc156fc33e
Trackster: only allow datasets with proper dbkey to be added to visualization. This is a regression because summary data format [bigwig] requires a proper dbkey.
2013-11-14 11:00:19 -05:00
Aysam Guerler
9f97bad68d
UI: Fix async submit of grids
2013-11-14 02:31:07 -05:00
Jeremy Goecks
b66bcfda56
Merge stable branch to default.
2013-11-13 18:42:54 -05:00
Jeremy Goecks
8e9333b5a2
Implement a hack to avoid infinite recursion in custom builds.
2013-11-13 18:41:23 -05:00
Jeremy Goecks
b6827fb068
Implement a hack to avoid infinite recursion in custom builds.
2013-11-13 18:41:23 -05:00
John Chilton
d0a8865981
LWR: Expand user properties (__user_name__, __user_email__, __user_id__) in job params before creating client.
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This was final piece of puzzle for running jobs as real user through LWR. Now on just needs to add <param id="submit_user">$__user_name__</param> to LWR destination in job_conf.xml on Galaxy side to pass this information to the LWR. More complicated on the LWR side obviously, need to configure DRMAA, set job manager to be 'queued_external_drmaa', and setup sudo rules. Will add some details to LWR documentation shortly.
2013-11-13 16:37:11 -06:00
Greg Von Kuster
582f08577b
Improved temporary directory management in the Tool Shed.
2013-11-13 16:17:33 -05:00
Dave Bouvier
39247d7cec
When running the install and test framework, explicitly uninstall any tool dependency that is not in the state Installed.
2013-11-13 14:46:25 -05:00
Dave Bouvier
2f6982eac4
Merge in fix from stable.
2013-11-13 14:18:36 -05:00
John Chilton