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2250 Commits
Author SHA1 Message Date
Daniel Blankenberg 126ae073af Enable multi-part upload for the GenomeSpace export tool. Files greater than 5gb can once again be send to GenomeSpace from Galaxy. 2015-04-02 13:49:36 -04:00
Daniel Blankenberg feb0a26f8d Some basic Caching for the GenomeSpace Export Tool's list of available target directories, so we don't have to reload and download everything every time, especially now that we are calling the parameter's get options method 5 times (6 on reload) when a user loads the tool interface. For now, we'll use 30 seconds as the cache valid time length. 2015-03-17 13:08:06 -04:00
peterjc aafd2d0a51 Add sorting option to Count1 (tools/filters/uniq.xml) 
When using this tool to produce a tally table, often want to
have the most common entries listed first - rather than the
sort order coming from the values being counted.
 2015-03-13 16:43:02 -04:00
peterjc fc58d3d781 Fix trailing space removal 
I had a test case which showed the problem, I just over looked it.

The input file species_assignment.tabular now includes more trailing
space examples columns 2, 3 and 4 to make this visually clearer at
first glance (previously the single trailing space example was
too easily overlooked).
 2015-03-13 16:43:02 -04:00
peterjc 1317cf8a84 Remove trailing comma space in uniq.py stdout 
$ python tools/filters/uniq.py -i test-data/species_assignment.tabular -o test-data/species_assignment_c2.tabular -c 2 -d T
Count of unique values in c2,

$ python tools/filters/uniq.py -i test-data/species_assignment.tabular -o test-data/species_assignment_c2c3.tabular -c 2,3 -d T
Count of unique values in c2, c3,

becomes:

$ python tools/filters/uniq.py -i test-data/species_assignment.tabular -o test-data/species_assignment_c2.tabular -c 2 -d T
Count of unique values in c2

$ python tools/filters/uniq.py -i test-data/species_assignment.tabular -o test-data/species_assignment_c2c3.tabular -c 2,3 -d T
Count of unique values in c2, c3
 2015-03-13 16:43:01 -04:00
peterjc 9f18034805 Do not remove spaces in Count1 (tools/filters/uniq.xml), with tests 
Also sets the tool version for the first time, using 1.0.1.

$ python tools/filters/uniq.py -i test-data/species_assignment.tabular -o test-data/species_assignment_c2.tabular -c 2 -d T
Count of unique values in c2,

$ python tools/filters/uniq.py -i test-data/species_assignment.tabular -o test-data/species_assignment_c2c3.tabular -c 2,3 -d T
Count of unique values in c2, c3,
 2015-03-13 16:43:01 -04:00
peterjc fce2184e5b Make tool version explicit (Job runner would assume 1.0.0) 2015-03-09 15:21:48 +00:00
John Chilton 77b167bbd1 Comment out broken liftOver tests. 
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) 
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) 
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