Ross Lazarus
c84dd733f0
Hack to fix the ghost broken dataset problem after uploading a composite file
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Delete any precreated datasets leftover..
2010-05-11 13:25:39 -04:00
Ross Lazarus
aaca176ed7
Add mimetypes to snp/wga datatypes in genetics.py
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Fix edit_attributes to snp/wga composite files in tests
2010-05-11 11:51:49 -04:00
Nate Coraor
37cf5fa7f3
Add worker threads to SGE runner
2010-05-10 20:59:41 -04:00
James Taylor
341b824044
Fix for exporting workflows with input dataset modules
2010-05-10 14:30:18 -04:00
Nate Coraor
2bd25bf652
Remove builds.txt from source control - use builds.txt.sample instead and copy it over if you don't have one
2010-05-10 12:50:09 -04:00
Jeremy Goecks
ef6ac7b90c
Add 'filter transcripts via tracking' tool to RNA-seq tools. This tool is useful for operating on output files from cufftools suite.
2010-05-10 12:42:05 -04:00
Ross Lazarus
40f4cba174
right welcome.html at last
2010-05-10 11:55:08 -04:00
Ross Lazarus
c23c237633
Revert inadvertantly updated tool_conf.xml.sample and welcome.html
2010-05-10 11:49:25 -04:00
Nate Coraor
ac033db509
Bug in SGE external metadata
2010-05-10 11:22:50 -04:00
Nate Coraor
273861ace3
Add external metadata to SGE
2010-05-10 11:13:51 -04:00
Ross Lazarus
afec1f9c3a
SNP/WGA tool changes only
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Updates to functional test outputs
Minor tweaks to some tests
All now pass when run using -sid but there's something busted when a full functional test is run
2010-05-10 10:17:11 -04:00
Ramkrishna Chakrabarty
4c8f98b627
lims:
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default view of requests page now shows requests belonging to any state
2010-05-10 10:03:00 -04:00
Jeremy Goecks
8d5148de47
Clean up annotation display for workflow steps.
2010-05-09 22:37:50 -04:00
Kanwei Li
b83afd1dfb
trackster: fix track saving
2010-05-07 18:25:29 -04:00
Jeremy Goecks
815fd36e51
Another update to search+select: pack script and replace icon.
2010-05-07 10:28:28 -04:00
Jeremy Goecks
7f86345e99
Replace large selects w/o refresh_on_change with search+select.
2010-05-07 09:16:51 -04:00
Jeremy Goecks
6bf9aa4c32
Fix grid filtering bug.
2010-05-07 08:52:43 -04:00
Greg Von Kuster
53363c793e
Add the modENCODEfly and modENCODEworm data source tools.
2010-05-06 19:39:27 -04:00
Jeremy Goecks
bc87138dca
Fix bug that was preventing annotation of workflow input datasets.
2010-05-06 17:52:49 -04:00
Kanwei Li
25b041ef16
trackster:
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- Custom dbkeys now create new HDA and copies info in
- Fix track reordering for all browsers
- Fix track deletion
- Fix BAM display
2010-05-06 12:30:54 -04:00
Kelly Vincent
dbfa0a7cca
Updated builds.txt (and manual_builds.txt) to newest version, corresponding to that on main. Includes hg19 and phiX correction.
2010-05-06 12:11:47 -04:00
Jeremy Goecks
ae522e303e
Update documentation in cufftools wrappers.
2010-05-06 10:58:23 -04:00
Ramkrishna Chakrabarty
a983fdb2ab
lims: workflow selectbox in the samples page fixed
2010-05-06 10:43:13 -04:00
Greg Von Kuster
7b0207bc01
Fix for downloading a library dataset from the library dataset's info page.
2010-05-06 10:08:57 -04:00
Kelly Vincent
1c56e2e768
Enhanced column join to allow user to specify fill values for empty columns, either one value for all or by column
2010-05-05 11:34:29 -04:00
Jeremy Goecks
07f96e096d
Fix bug that mucked up fetch for chrom lengths in new track browsers.
2010-05-04 22:27:05 -04:00
Jeremy Goecks
bfff008170
Removing debugging msg.
2010-05-04 21:57:26 -04:00
Kanwei Li
0a7d97952c
trackster: fix BAM data error; display tweaks
2010-05-04 15:43:34 -04:00
Greg Von Kuster
4eb385da54
Fix the recentrly introduced grid filter / search bug. Revert the recently introduced grid filter_params hack for generating links since we now use a different approach to rendering links. Convert a few more 'message_type' params to be 'status' instead. Many fixes for the community space app.
2010-05-04 14:21:21 -04:00
Dannon Baker
b082109c1c
Secure=True by default for workflows.
2010-05-04 14:19:44 -04:00
Jeremy Goecks
01e3500711
Update types for cuffcompare output files.
2010-05-04 13:45:57 -04:00
Kanwei Li
7ce4296230
trackster: add filled line display
2010-05-04 12:50:48 -04:00
Nate Coraor
ca066cef04
Add a tip to the upload tool about using url paste for big files
2010-05-04 10:18:42 -04:00
James Taylor
2a141b0caa
Very basic support for exporting and importing workflows among instances
2010-05-03 17:35:54 -04:00
Jeremy Goecks
6dcf593af8
Enable users not logged in to view a shared/accessible/published visualization.
2010-05-03 16:32:35 -04:00
Nate Coraor
592435e175
Community: add help for tool-related operations
2010-05-03 15:33:34 -04:00
Jeremy Goecks
1b3280da58
Pack scripts.
2010-05-03 14:03:01 -04:00
Jeremy Goecks
2b94fd683b
Enable viewing of shared/accessible/published visualizations.
2010-05-03 14:02:08 -04:00
Ramkrishna Chakrabarty
de22cb1c51
forms default value bug fixed
2010-05-03 09:42:51 -04:00
Ramkrishna Chakrabarty
688e0a7316
lims:
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request page now shows a msg if the request has library selected
forms default value bug fixed
2010-05-03 09:34:13 -04:00
Jeremy Goecks
06f1110d2a
Bug fixes for history import: (a) import can now be used by users who have access via sharing and (b) import changes the current history to the imported history. Functional tests updated to reflect new functionality and error messages.
2010-05-02 15:34:41 -04:00
Jeremy Goecks
be8296b043
merge
2010-04-30 18:26:49 -04:00
Jeremy Goecks
19f9bafc7f
Cuffcompare wrapper handles all outputs gracefully. Tests needed.
2010-04-30 18:26:06 -04:00
Nate Coraor
b91b92f83f
Community: Add tool versioning and tighten up the requirements in the upload/approval process
2010-04-30 16:11:17 -04:00
Kelly Vincent
4279bd99b4
Fix dbkey setting for BWA.
2010-04-30 15:45:32 -04:00
Kelly Vincent
139c2cf667
Change the way size of output file determined in Bowtie and SAM-to_BAM to deal with memory limitation.
2010-04-30 15:27:41 -04:00
Greg Von Kuster
675d3bed06
Add a link to the user's uploaded tools from the Manage users grid, and fix some more bugs in the community app.
2010-04-30 15:20:04 -04:00
Greg Von Kuster
cdfaa79090
Many fixes and additional features added to the community.
2010-04-30 14:08:23 -04:00
Jeremy Goecks
0a4348a661
merge
2010-04-30 13:09:29 -04:00
Jeremy Goecks
4aeef6f862
Remove headers from SAM file so that output matches new Tophat wrapper.
2010-04-30 13:08:33 -04:00
Ross Lazarus