opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity
15,827 Commits 69 Branches 243 Tags
482e0ce0fa2fa5d43ffac71ea6ac98747007fa40
Commit Graph
2238 Commits
Author SHA1 Message Date
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) 
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. 
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. 
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. 
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. 
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. 
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) 
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
Clayton Turner 9e86f172bc Merge from stable 2014-02-10 16:49:43 -05:00
Clayton Turner 7347d75a4a Added ignore lines starting with specific characters to group tool 2014-02-10 16:00:30 -05:00
Daniel Blankenberg 040fb029f8 Update GenomeSpace import tools to use current working directory instead of __new_file_path__ for extrafiles created using multiple outputs technique. Should resolve issue on our public servers where only the first selected file was being imported to the history. 2014-02-05 13:44:32 -05:00
Dannon Baker 832d0c7985 Merged in nsoranzo/galaxy-central (pull request #312) 
Remove unused imports and unused variables. Fix spacing.
 2014-02-04 10:33:40 -05:00
Nate Coraor 9c64fc123e Remove broken and/or obsolete tools. 2014-01-27 13:58:31 -05:00