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Author SHA1 Message Date
John Chilton 321cd78ad8 Merge pull request #5512 from mvdbeek/fix_new_pysam 
[18.01] Make galaxy compatible with pysam 0.14
 2018-02-13 11:22:04 -05:00
mvdbeek 3b8a2f9edc Pin pysam to 0.14 2018-02-13 15:22:51 +01:00
mvdbeek 349b25b74a Minimize duplication of BAM set_meta code 2018-02-13 11:49:10 +01:00
Nate Coraor aefe0e1449 Merge pull request #5510 from martenson/ts-deny-codefile 
[18.01] do not allow codefiles for TS tool loading
 2018-02-12 16:46:11 -05:00
mvdbeek b87d57aac7 Make galaxy compatible with pysam 0.14 2018-02-12 22:03:49 +01:00
Martin Cech ba3b3d5c18 do not allow codefiles for TS tool loading 2018-02-12 14:06:50 -05:00
Björn Grüning c5568a7b1a Merge pull request #5467 from dannon/workflow_sharing_link_fixes 
[18.01] Workflow sharing link fixes
 2018-02-11 11:49:55 +01:00
Dannon Baker d91078024b Merge pull request #5491 from nsoranzo/release_18.01_fix_common_startup_for_bare_clone 
[18.01] Fix common_startup.sh for galaxy tarballs
 2018-02-08 13:20:46 -05:00
Dave B 3f50b45a4e Merge pull request #5445 from gregvonkuster/add-ideaspre 
[18.01] Add support for the ideaspre datatype
 2018-02-08 13:11:10 -05:00
Nicola Soranzo eba3fb4b35 Fix common_startup.sh for galaxy tarballs 
Do not assume git is installed and the `.git` directory is present.

Fix https://github.com/galaxyproject/galaxy/issues/5466
 2018-02-08 11:52:24 -05:00
Nate Coraor 977bbf1481 Install node and yarn in common_startup.sh using nodeenv and the venv's 
npm.
 2018-02-08 11:33:55 -05:00
Nate Coraor b463be78a5 Add nodeenv to dev requirements 2018-02-08 11:33:35 -05:00
John Chilton 64e4e8b572 Merge pull request #5482 from mvdbeek/bam_recursion_bug 
[18.01] Fix recursion bug in BamNative datatype
 2018-02-08 08:14:48 -05:00
John Chilton e9ed97f533 Merge pull request #5485 from scholtalbers/fix/#5484_rename_post_actions 
[18.01] Fix #5484
 2018-02-08 08:11:51 -05:00
Jelle Scholtalbers db069198af fix #5484 2018-02-08 10:42:31 +01:00
Marius van den Beek 8b0e3bd28f Fix recursion bug in BamNative datatype 
We introduced this in
https://github.com/galaxyproject/galaxy/pull/5180/ where we moved a lot
of code form the Bam class into the BamNative class.

Reported by @natefoo
 2018-02-07 23:00:44 +01:00
Dannon Baker 62540a9747 Merge pull request #5470 from natefoo/revert-5036 
[18.01] Revert #5036
 2018-02-07 14:49:06 -05:00
Nate Coraor 11ec4ee93d Revert "Try next dep. resolver if building env failed" 
This reverts commit e821d469e6.
 2018-02-07 13:16:18 -05:00
Nate Coraor 04e4da0d31 Revert "Avoid duplicate dependency installation" 
This reverts commit c0cf41a15c.
 2018-02-07 13:16:11 -05:00
Dannon Baker 9df2813524 Fix more workflow sharing broken links 2018-02-07 12:45:40 -05:00
Dannon Baker 7feef3dc0e Fix "Go back to workflows list" link on workflow sharing interface. 2018-02-07 12:45:40 -05:00
Nate Coraor c2abd3f813 Merge pull request #5395 from martenson/production-1801 
[18.01] Build production client
 2018-02-05 16:49:09 -05:00
Dannon Baker c3ada7f169 Merge pull request #5460 from jmchilton/fix_oom_parse 
[18.01] Fix tool stdio level parsing for OOM level.
 2018-02-05 15:04:30 -05:00
Martin Cech d537b2ac60 build client for release with maps 2018-02-05 14:28:03 -05:00
Dannon Baker f0a8243f7d Client-format post-merge 2018-02-05 13:06:29 -05:00
Dannon Baker 0704d63d0b Merge remote-tracking branch 'jmchilton/1801_hdca_delete' into release_18.01 2018-02-05 13:06:01 -05:00
John Chilton 2f020ef944 Fix tool stdio level parsing for OOM level. 
Backend was enhanced to allow this in #5196 and a new entry point to setting exit code for such exit conditions but the custom parsing wasn't updated to allow it. Thanks to @nsoranzo for the catch.
 2018-02-05 12:18:22 -05:00
Dannon Baker 2cb3af5d60 Merge pull request #5447 from natefoo/server-name-fix 
[18.01] Fix server_name when config is a dict
 2018-02-05 10:43:03 -05:00
Martin Cech b28fb7e4d7 change the history icon-btn selector to work with dropdowns 2018-02-04 20:10:36 -05:00
Dannon Baker 207f5faba0 Merge pull request #5449 from jmchilton/collection_mapping_fixes 
[18.01] Collection mapping fixes for regression in 18.01.
 2018-02-04 11:52:33 -05:00
John Chilton b2e8d891b7 Merge pull request #5456 from mvdbeek/fail_job_fix_when_tool_unavailable 
Fix setting job failure exception
 2018-02-03 15:01:17 -05:00
John Chilton 51e030f4f3 Bring in @mvdbeek's test cases from #5431. 2018-02-03 14:59:30 -05:00
John Chilton f99299f833 Pre-compute more collection state during mapping. 
Still dealing with fallout from 78babab645. After that commit we were treating structured_like collections like collections with unknown structure and not dealing with collection_type_source information at all when building backbones for new collections during mapping.
 2018-02-03 14:59:30 -05:00
mvdbeek 7bbc46658a Fix setting job failure exception 
This can happen when the job's tool is unavailble and
outputs_to_working_directory is activated.
Fixes https://github.com/galaxyproject/galaxy/issues/5424.
 2018-02-03 18:09:57 +01:00
Martin Cech 1bd8c4fd26 Merge pull request #5455 from jmchilton/backport_flakey 
[18.01] Backport: Add --skip_flakey_fails flag to CI script for API tests
 2018-02-03 11:45:16 -05:00
Nicola Soranzo 935b8c948c Add --skip_flakey_fails flag to CI script for API tests 
xref. https://github.com/galaxyproject/galaxy/pull/5286#issuecomment-358404551
and following comments.
 2018-02-03 08:11:46 -05:00
Marius van den Beek 5aed347c30 Merge pull request #5418 from jmchilton/collection_pja 
[18.01] Implement more intuitive collection PJA
 2018-02-03 09:55:24 +01:00
Nate Coraor dac1ba5812 Fix failing integration tests for workflow handlers. 2018-02-02 15:40:22 -05:00
Martin Cech 3512096a14 remove unused classes and aria 2018-02-02 13:53:26 -05:00
Martin Cech 8019afb8b5 fix typo 2018-02-02 13:34:17 -05:00
Martin Cech 55b6d601a8 add empty href to links so the cursor is right 2018-02-02 13:32:56 -05:00
John Chilton 8e32e93d6d Implement more collection workflow post job actions. 
Implement hide, delete, add tag, and remove tag for output collections and mapped over collections.

Fixes https://github.com/galaxyproject/galaxy/issues/1680.
 2018-02-02 13:29:57 -05:00
greg 3fdd4edc5c Subclass IdeasPre from Html 2018-02-02 13:07:52 -05:00
Nate Coraor b0162ba543 Fix server_name when config is a dict. 2018-02-02 12:53:39 -05:00
Marius van den Beek fbfbdd51bb Merge pull request #5416 from jmchilton/rename_collections_pja 
[18.01] Fix rename post job actions to be more intuitive when mapping over collections.
 2018-02-02 17:53:37 +01:00
Marius van den Beek 6c013d0cb3 Merge pull request #5444 from dannon/multidelete_fix 
[18.01] Ensure jobStateSummariesCollection exists;
 2018-02-02 17:51:27 +01:00
John Chilton 0529153ac0 Fix bug in PJAs for collection mapping. 
Reported by @mvdbeek here (https://github.com/galaxyproject/galaxy/pull/5416#issuecomment-362194157).
 2018-02-02 09:54:30 -05:00
John Chilton f6f9f9a891 Extend mapped collection output rename PJAs to include # replacements. 
Also make sure output collections in non-mapping scenarios are also properly renamed as well.
 2018-02-02 09:52:44 -05:00
John Chilton 2b8df110d0 Apply rename PJA to collection outputs including $ replacements. 
Update PJA collection test to test HDCA is renamed also.
 2018-02-02 09:52:44 -05:00
greg b5945ad3e3 Add IdeasPre datatype subclassed from Rgenetics 2018-02-02 09:22:10 -05:00