 Nicola Soranzo
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d1bc98dfcb
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Python3: fix remaining print statements
Remove some debugging prints.
Fix import order.
Consolidate exception logging in ToolShed database migrations.
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2017-10-12 18:34:29 +01:00 |
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Nicola Soranzo
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21b44bf348
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Fix all E201 and E202 style errors
using the following command:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 .
```
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2017-08-17 11:35:39 +01:00 |
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Nicola Soranzo
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d85db9daa6
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Use __file__ when adding paths to sys.path instead of os.getcwd() .
Also insert additional paths in position 1 unless strictly necessary.
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2016-02-18 15:45:15 +00:00 |
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Nicola Soranzo
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6569c2dcc3
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Partially lint scripts/ .
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2015-07-13 20:13:28 +01:00 |
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Dave Bouvier
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35bc12d769
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Migrate tools from the distribution to the tool shed.
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2014-07-28 11:58:52 -04:00 |
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Dave Bouvier
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a3018feb02
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Migrate 22 tools from the distribution to the tool shed.
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2014-05-19 13:01:46 -04:00 |
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Greg Von Kuster
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d818047609
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Change the name of the current InstallManager to the more appropriate ToolMigrationManager since it handles only tool migrations. This allows for the InstallManager to be used for more general Tool Shed install processes.
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2014-05-06 10:34:28 -04:00 |
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Dave Bouvier
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7007f8594c
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Fixed tool help image for gops complement.
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2014-04-14 13:17:12 -04:00 |
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Dave Bouvier
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c7e6181c20
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Fix issues with tool migration stage 10.
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2014-04-14 09:32:41 -04:00 |
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Dave Bouvier
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7da3f0a6aa
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Corrected version for migrated tools.
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2014-04-10 13:59:40 -04:00 |
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Dave Bouvier
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db12448003
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Fixed JAVA_JAR_PATH for realigner_target_creator.
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2014-04-04 10:37:52 -04:00 |
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Dave Bouvier
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463b50bb1d
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Use correct revisions of best_regression_subsets and weightedaverage.
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2014-04-03 09:45:51 -04:00 |
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Dave Bouvier
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b6af887925
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Corrected an error in the analyze_covariates tool shed repository.
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2014-04-02 16:05:57 -04:00 |
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Dave Bouvier
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83af05b1f2
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Migrate 46 tools from the distribution to the tool shed: gatk, gops, regional variation.
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2014-04-01 11:04:32 -04:00 |
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Dave Bouvier
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85add8fc6d
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Fix path for bowtie2.
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2014-02-20 23:01:05 +00:00 |
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Dave Bouvier
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665099efa4
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Situations where a migration warning would be incorrectly displayed, and tools with matching filenames would be removed from the tool_conf.xml after running a migration script.
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2014-02-19 15:23:45 -05:00 |
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Dave Bouvier
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3ec4601e8d
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Fix description for find_diag_hits.
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2014-01-27 10:44:24 -05:00 |
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Dave Bouvier
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448d9f55eb
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Migrate 43 tools from the distribution to the tool shed.
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2014-01-27 09:53:14 -05:00 |
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Dave Bouvier
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962be8d8ec
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Remove sam_fa_indices.loc.sample from tool-data. Update migration xml to the correct revisions of cufflinks repositories.
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2013-10-01 15:49:08 -04:00 |
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Dave Bouvier
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695aa8f44d
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Migrate cuffcompare, cuffdiff, cufflinks, and cuffmerge from the distribution to the tool shed. Update the 'Review migration stages' layout.
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2013-10-01 13:54:57 -04:00 |
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Dave Bouvier
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b0efe4ddea
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Migrate tools from the distribution to the tool shed, including but not limited to samtools and fastx_toolkit tools.
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2013-09-26 10:05:00 -04:00 |
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Greg Von Kuster
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0a704cdb6d
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Automatically eliminate tool entries from non-shed-related tool panel configs for tools contained in tool shed repositories that were migrated out of the Galaxy distribution.
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2013-08-22 10:12:08 -04:00 |
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Greg Von Kuster
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280125ee99
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Move ~/lib/galaxy/tool_shed to ~/lib/tool_shed, and move the ~/lib/galaxy/util/shed_util componets to ~/lib/tool_shed/util.
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2013-02-26 15:52:51 -05:00 |
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Greg Von Kuster
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1c7ef874b5
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Utility code cleanup and import tweaking.
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2012-12-13 11:41:31 -05:00 |
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Dave Bouvier
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576ceb7829
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Revert tool migration.
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2012-12-07 16:38:26 -05:00 |
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Dave Bouvier
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de7cb21382
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Migrate tools to tool shed: addValue, ChangeCase, Condense characters1, Convert characters1, Cut1, mergeCols1, Remove beginning1, Show beginning1, Show tail1, trimmer
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2012-12-07 16:08:40 -05:00 |
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Dave Bouvier
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917d5a72e8
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Migrated lastz and bowtie tools to the tool shed. Added a target_file feature to the tool dependency installation process.
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2012-11-26 10:18:47 -05:00 |
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Greg Von Kuster
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d0438ecb2f
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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.
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2012-11-07 10:51:35 -05:00 |
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Dave Bouvier
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cc608c31b2
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Updated migration script to reference repository with correct use of tool dependency tag sets.
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2012-10-25 13:25:39 -04:00 |
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Dave Bouvier
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c968460662
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Migrate Picard tools to the tool shed.
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2012-10-24 11:09:20 -04:00 |
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Dave Bouvier
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c2eeee7b9f
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Migrate BWA to the tool shed.
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2012-09-28 15:35:44 -04:00 |
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Dannon Baker
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3d5fd7b5e2
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Migrate NCBI Blast+ (and blastxml) to the toolshed.
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2012-08-17 11:35:31 -04:00 |
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Greg Von Kuster
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7992dfa449
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Another change to installed changed revision for the freebayes tool migration process.
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2012-07-13 12:53:42 -04:00 |
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Greg Von Kuster
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2c87a63983
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Change ethe installed changed revision for the freebayes tool migration process.
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2012-07-13 12:50:29 -04:00 |
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Greg Von Kuster
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5c8fe01456
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Migrate the freebayes tool out of the Galaxy code distribution.
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2012-07-10 16:23:34 -04:00 |
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Greg Von Kuster
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3c5f027a73
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Enable the installation of the emboss_5 repository from the tool shed under the condition that any of its contained tools are defined in a local tool_conf.xml file.
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2012-03-21 16:53:26 -04:00 |
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Greg Von Kuster
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7ebdf0f24a
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More fixes for handling mor ethan one non-shed tool anel config when installing tools migrated from the distrobution to the tool shed.
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2012-03-15 14:12:59 -04:00 |
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Greg Von Kuster
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628b6ea82d
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Use an odict instead of a dict when acquuiring elements for generating entries for the migrated_tools_conf.xml from the InstallManager, and handle multiple proprietary non-shed tool panel configs with the InstallManger.
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2012-03-15 11:47:46 -04:00 |
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Greg Von Kuster
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e0942033ba
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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.
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2012-02-28 11:38:08 -05:00 |
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