John Chilton
88239abf5c
Add more distribution tool citations.
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xref #361 .
2015-10-05 15:16:50 +01:00
Nicola Soranzo
34d9388456
Use os.pardir everywhere instead of '..' .
2015-07-14 16:20:29 +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.
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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.
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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.
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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
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
peterjc
fce2184e5b
Make tool version explicit (Job runner would assume 1.0.0)
2015-03-09 15:21:48 +00:00
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
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
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
6d4d6dd91a
Bugfix: Fix shutil.move for converted files in upload.py.
2014-06-10 09:36:28 -05:00
Daniel Blankenberg
3f78f9a449
Re-add InterMine tools removed in 401ee23dcf2f70d4be0e975bb3e00a43ae1dfdd0.
2014-06-27 14:44:55 -04:00
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
Nicola Soranzo
f73d5fba6c
Fix old wiki links.
2014-04-10 20:00:45 +02:00
Trevor Wennblom
1848cf2e3d
whitespace
2014-02-20 18:14:09 -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
Nate Coraor
9c64fc123e
Remove broken and/or obsolete tools.
2014-01-27 13:58:31 -05:00
John Chilton
323a7c57c7
Fix for b1121a315205e8152d9c59199443c492340e9f0b.
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That did not work in Bjoern's setup for reasons that still are eluding me - but this variant works and is less hacky, more readable anyway.
2014-01-20 08:35:50 -06:00
John Chilton
915948a305
Hide to_posix_lines in UI by default.
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Galaxy still completely supports this option on backend - API tests still completely work and will hopefully ensure this functionality continues running. Any Galaxy deployements that wish to enable this option simply have to switch this one param from hidden to select. This is a ugly workaround - but it is a very small workaround - and will hopefully alleviate any potential fears Gert Hulselmans has of Galaxy diverging from his changes. This is only a stop gap until the Galaxy upload UI supports more advanced options.
I have previously outlined my concerns with the visual clutter on the upload.xml page - this is why I am hiding it by default. If anyone with commit access disagrees - please by all means backout of this individual changeset and restore the full functionality of pull request 171 (I have a terrible eye for this sort of GUI design stuff).
2014-01-17 00:03:26 -06:00
John Chilton
658ea5966c
Merge pull request 171.
2014-01-16 23:57:43 -06:00
Nate Coraor
607fc002ea
Fix outdated usage of states in microbial dataset post-job hook.
2013-10-10 12:53:10 -04:00
Nate Coraor
705457f218
Convert DOS line endings.
2013-10-10 12:48:07 -04:00
Greg Von Kuster
f9a701164e
Fix inadvertently committed Galaxy upload tool config setting ajax upload to false.
2013-07-12 11:13:27 -04:00
Greg Von Kuster
2ae17f816d
Allow public usernames in the tool shed to be a minimum of 3 characters.
2013-07-06 19:41:10 -04:00
Daniel Blankenberg
33fd08a1a5
Change EBI SRA tool to use auto detect for format determination now that they are providing additional formats. Fixes issue seen when sending SFF files.
2013-06-26 11:57:51 -04:00
Gert Hulselmans
fb01c3cc96
Avoid corruption of binary files embedded in gzip, bz2 and zip archives in the upload tool.
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Add an option in the upload tool to disable the conversion of universal
line endings to Posix line endings.
This is useful for avoiding corruption of uploaded files when a binary
file is contained inside a gzip, bz2 and zip archive.
This fixes bug report: https://trello.com/card/issue-with-uploaded-2bit-gz-files/506338ce32ae458f6d15e4b3/702
2013-05-27 20:55:52 +02:00
Dannon Baker
8161b70d89
Merged in nsoranzo/galaxy-central (pull request #135 )
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Add generic ASN.1 text and binary datatypes
2013-04-04 08:41:54 -04:00
Nicola Soranzo
2f650b8866
Fix file extension determination
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Extension was determined uncorrectly for filenames with more than 1 dot
2013-03-06 12:37:08 +01:00
John Chilton
262413f7c0
Based on input from natefoo, replace root tool tag "upload" with inverse tag "workflow_compatible". Adjust logic in tools module accordingly.
2013-02-13 10:45:56 -06:00
John Chilton
7e6ee45bb0
Add optional "upload" attribute to tool definitions.
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When extracting workflows, such tools are treated as inputs. This eliminates the need for the hack of hardcoding 'upload1' in tools.py and allows multiple upload tools to exist and function properly when extracting workflows.
2013-02-10 11:13:51 -06:00
Daniel Blankenberg
a2a1a15b6f
Add MouseMine datasource tool provided by Howie Motenko (Howie.Motenko@jax.org).
2013-02-06 17:34:36 -05:00
Daniel Blankenberg
a273960126
Backout 3189a1bf18af
2013-02-04 06:43:35 -05:00
Daniel Blankenberg
bab984ed69
Add sentry_dsn to Tool Shed config.py' lib/galaxy/webapps/community/config.py
2013-02-04 06:33:19 -05:00
Kyle Ellrott
4aad0ad15e
Enabling dataset UUID setting through library upload, upload1 tool, and galaxy.json file
2013-01-29 15:58:58 -08:00
Brad Chapman
cf1407d471
Correctly set history and handle output datasets for error cases in tool API. Allow specification of dataset name during uploads, exposing through API
2012-10-04 15:31:16 -04:00
John Chilton
886a5c61b9
Merge.
2012-09-03 22:14:36 -05:00
Daniel Blankenberg
48548341fc
Handle non-ascii unicode in upload tool. Significant pre-existing refactoring still needed.
2012-08-28 19:23:39 -04:00
Daniel Blankenberg
d84ab3226e
Handle non-ascii unicode in data source tools. Add util.is_binary() method that returns true when provided string contains a null byte.
2012-08-28 19:23:39 -04:00
John Chilton