John Chilton
77b167bbd1
Comment out broken liftOver tests.
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liftOver loc file handling is problematic (https://trello.com/c/A6I6zQvF ). If it weren't this wouldn't be a problem. I could fix the API functional test framework to mimic the older form driven approach but it would take a week and would be rendered moot by fixing liftOver. Unfortunately, fixing liftOver would likely break a lot of existing workflows and tool reruns so I am not fixing that either.
Only option left, admittedly a crappy one, is to comment out the tests.
2015-02-23 23:09:19 -05:00
Dannon Baker
04bd3c77c1
Merged in dan/galaxy-central-prs (pull request #643 )
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Add ZebrafishMine Data Source Tool.
2015-02-02 12:04:23 -05:00
Daniel Blankenberg
538c07cc49
Add ZebrafishMine Data Source Tool.
2015-01-21 14:56:08 -05:00
Bjoern Gruening
5b96f80b48
Add CompressedArchive as datatype and do not uncomress it during upload.
2015-01-12 22:36:20 +01:00
Daniel Blankenberg
b022e92f5b
Add gemini.sqlite datatype.
2015-01-09 14:48:56 -05:00
Björn Grüning
ccdd1207fb
Add rpy requirement.
2014-11-14 14:56:28 +00:00
Martin Cech
709abedcb4
Merged in anton/galaxy-central-anton (pull request #539 )
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Initial tweaks to tool_conf.xml sample and one of the tools.
2014-11-11 12:26:45 -05:00
Nicola Soranzo
3c60edfda7
Add Graph2 output dataset when "-read_trkg yes".
2014-10-28 17:15:39 +01:00
Nicola Soranzo
0af9b67d07
Use from_work_dir instead of copying output files line by line. Write velvetg output to stdout.
2014-10-28 18:45:17 +01:00
Nicola Soranzo
fbcf3e2bbc
Make stripping and condensing optional.
2014-10-28 16:57:49 +01:00
Nicola Soranzo
526c2507d7
dos2unix
2014-10-28 12:21:00 +01:00
Anton Nekrutenko
873d1f455c
uniq.xml edited online with Bitbucket
2014-10-23 16:42:15 +00:00
John Chilton
34e1273f9b
Rework pull request #489 memory handling to respect deployer set _JAVA_OPTIONS.
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As discussed here https://bitbucket.org/galaxy/galaxy-central/pull-request/489/srma-tool-requires-at-least-2048m-memory/diff . Thanks to Bjoern for input.
2014-09-22 13:20:49 -04:00
John Chilton
0a9d671f52
Merge pull request #489 .
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Thanks Lance!
2014-09-22 13:17:11 -04:00
Nate Coraor
e56943de8c
Always access UCSC Main via HTTPS.
2014-09-22 11:31:56 -04:00
John Chilton
4a17892400
Always access EBI SRA via HTTPS.
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Thanks to Ilya for opening pull request to make it conditionally use HTTPS - https://bitbucket.org/galaxy/galaxy-central/pull-request/491/remove-http-from-ebi-url-which-is/diff - but this goes one step further and always uses HTTPS as suggested by Nate in the pull request comments.
2014-09-22 11:23:02 -04:00
Dannon Baker
9d85ca9e23
Switch to_json_string/from_json_string in galaxy/tools.
2014-09-09 10:06:35 -04:00
Lance Parsons
d0dbaa377d
Made regex more specific
2014-09-05 10:55:38 -04:00
Lance Parsons
0a3e5d274f
SRMA tool requires at least 2048m memory and LENIENT validation stringency
2014-09-04 16:12:51 -04:00
Lance Parsons
94e2961e30
Allow specification of complete filename of 2bit files in codingSnps.pl
2014-09-04 16:02:54 -04:00
Daniel Blankenberg
8ccf8287b4
Quote commandline arguments for extract genomic DNA tool.
2014-09-02 13:15:17 -04:00
Kyle Ellrott
9d67f9c599
Hiding UUID input for upload tool
2014-08-18 16:37:30 -07:00
Kyle Ellrott
a2ac71eab9
Enabling UUID in file upload
2014-08-14 17:08:29 -07:00
John Chilton
57ea16b55d
Fix more BibTeX problems caught by @peterjc.
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See https://bitbucket.org/galaxy/galaxy-central/commits/3e8dfd372918c90ee4b37267f0b7c03a#comment-1140275 .
Thanks Peter!
2014-08-06 12:36:27 -04:00
John Chilton
5d89d0797f
Fix citation problem in 39c9831 caught by @peterjc.
2014-08-06 12:31:50 -04:00
John Chilton
8db7eed06a
Add annotated citations various tools.
2014-08-06 09:41:38 -04:00
John Chilton
4ddab82e9e
Add annotated citations for MAF tools.
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Add macro file to centralize this and in help citation description as well.
2014-08-06 09:41:38 -04:00
John Chilton
6d4d6dd91a
Bugfix: Fix shutil.move for converted files in upload.py.
2014-06-10 09:36:28 -05:00
Dave Bouvier
35bc12d769
Migrate tools from the distribution to the tool shed.
2014-07-28 11:58:52 -04:00
Björn Grüning
b9389cc76d
Add empty_field validator to gtf2bedgraph.xml
2014-06-27 22:21:37 +00:00
Daniel Blankenberg
3f78f9a449
Re-add InterMine tools removed in 401ee23dcf2f70d4be0e975bb3e00a43ae1dfdd0.
2014-06-27 14:44:55 -04:00
Dannon Baker
a6b6879f12
Reorder imports post-PR 403.
2014-06-09 10:53:00 -04:00
Saket Choudhary
769a1d4f49
PEP8 fixes, close find handles for 'convert delimiters to tab' tool
2014-06-09 11:56:06 +05:30
Dannon Baker
c30b7838cc
Fix for when check_binary fails against an actual binary datatype. The logic in upload needs to be revisited per the comments.
2014-06-02 13:16:15 -04:00
Dave Bouvier
a3018feb02
Migrate 22 tools from the distribution to the tool shed.
2014-05-19 13:01:46 -04:00
Daniel Blankenberg
4fdfc45156
Fixes for genomespace exporter recieving UnvalidatedValue objects.
2014-05-19 10:17:36 -04:00
Daniel Blankenberg
cb1f6c92f6
Update NGS read simulator to use job working directory.
2014-04-18 13:31:13 -04:00
Daniel Blankenberg
5e3e287ce3
Update MAF to BED to use job working directory and built-in primary dataset collection.
2014-04-18 13:23:38 -04:00
Daniel Blankenberg
213986aa7f
Update MAF to interval to use job working directory instead of __new_file_path__.
2014-04-18 12:34:08 -04:00
Nicola Soranzo
f73d5fba6c
Fix old wiki links.
2014-04-10 20:00:45 +02:00
Daniel Blankenberg
4d88ce03de
Improve handling of invalid/expired GenomeSpace tokens in GenomeSpace export tool.
2014-04-09 17:24:56 -04:00
Dave Bouvier
83af05b1f2
Migrate 46 tools from the distribution to the tool shed: gatk, gops, regional variation.
2014-04-01 11:04:32 -04:00
Daniel Blankenberg
745fa11661
Update GenomeSpace exporter directory listing to send the now working/required accept string.
2014-03-13 17:07:23 -04:00
Trevor Wennblom
1848cf2e3d
whitespace
2014-02-20 18:14:09 -06:00
John Chilton
f8bf5f4d8e
Merged in clayton_turner/galaxy-central (pull request #322 )
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Added "ignore lines starting with specific characters" to group tool
2014-02-20 10:35:58 -06:00
Aysam Guerler
ba0362aa8d
Add get data back to to tool panel (will be replaced by a placeholder soon)
2014-02-19 12:51:52 -05:00
Aysam Guerler
73e74f74c8
Upload: Hide former upload tool
2014-02-18 14:57:08 -05:00
Dave Bouvier
5f485f05b3
Remove tool that was migrated to the tool shed in 10719:c2f06b5cfba1. Remove test data that belonged to tools that were removed in 12288:401ee23dcf2f.
2014-02-17 13:05:00 -05:00
Dave Bouvier
ba17a35a99
Remove stats/wiggle_to_simple, which is an exact duplicate of filters/wiggle_to_simple.
2014-02-14 12:34:58 -05:00
Clayton Turner
fd85979a86
Fixed XML versioning and inputfile name
2014-02-14 12:25:20 -05:00
John Chilton