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
18,509 Commits 69 Branches 243 Tags
1fd38fb3ee467473d5326ef8c197cedcd9472d53
Commit Graph
2270 Commits
Author SHA1 Message Date
Nicola Soranzo 1830adfb30 Fixes for @jmchilton and @dannon. 2015-06-17 19:37:45 +01:00
Nicola Soranzo 7830bc62e0 Another fix for 3c40f32fa2 . 2015-06-17 19:21:13 +01:00
Nicola Soranzo 3c40f32fa2 PEP-8 and pylint fixes. 2015-06-16 16:53:49 +01:00
John Chilton 884e824d72 Merge remote-tracking branch 'vavrusa/table-datatype' into dev. 
Conflicts:
	lib/galaxy/datatypes/tabular.py
 2015-06-03 10:52:42 -04:00
John Chilton 1a39b6aa79 Merge remote-tracking branch 'jmchilton/release_15.05' into dev 2015-05-20 15:48:25 -04:00
Daniel Blankenberg af6172d14d Update default dbkey for worm_modencode.xml and bump version. 
ce10 is UCSC for WS220
 2015-05-20 12:42:05 -04:00
Daniel Blankenberg 93c51fa259 Update default dbkey for fly_modencode.xml and bump version. 
dm3 is UCSC for release 5
 2015-05-20 12:39:59 -04:00
Martin Cech 182fbd1bc6 fix the data source tools for modendcode with proper URLs 2015-05-19 16:53:25 -04:00
Nicola Soranzo 341a6cf760 Use requirements of type="package" instead of deprecated "binary". 2015-05-15 12:43:15 +01:00
Nicola Soranzo 224d8f3fc4 Remove numpy requirement, not used since commit 09ce7a9b17 . 2015-05-15 12:41:08 +01:00
Nicola Soranzo 22d4a1d8c3 dos2unix of tools/ directory. Some whitespace and PEP-8 fixes. 2015-05-15 12:40:52 +01:00
Marek Vavrusa bc8bdadca8 datatypes: extracted TabularData superclass from Tabular, CSV subclass 2015-04-30 17:20:32 +02:00
Björn Grüning 1dde01220c Remove plain R dependency 2015-04-29 21:49:04 +02:00
Marek Vavrusa e5aa966f1d stats/gsummary: RPy is deprecated, use RPy2/classic as an alternative 2015-04-29 17:24:22 +02:00
Björn Grüning 6f13a4be45 drop python-module 2015-04-29 16:47:37 +02:00
Björn Grüning e11e1864ef Update gsummary dependencies. 2015-04-29 12:14:07 +02:00
Dannon Baker 66ef2fc90e Merge over and resolve conflicts release->dev 2015-04-22 10:08:53 -04:00
Daniel Blankenberg 64fb5d15c1 Fix for GenomeSpace Exporter no longer allowing filenames to contain slashes. 2015-04-20 10:17:31 -04:00
Daniel Blankenberg 153bef1c52 Enable multi-part upload for the GenomeSpace export tool. Files greater than 5gb can once again be send to GenomeSpace from Galaxy. 
(cherry picked from commit 126ae073af)
 2015-04-16 09:48:42 -04:00
Daniel Blankenberg a25c5c025a 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. 
(cherry picked from commit feb0a26f8d)
 2015-04-16 09:48:35 -04:00
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