Daniel Blankenberg
ab53cc6d3b
First pass at adding Ensembl browsers as an external display application. Two different URL generation and data attachment methods are used; one for 'old' Ensembl archives older than ~November 2008 and another for Ensembl sites using the current method. The tool-data/shared/ensembl/ensembl_sites.txt file contains the site and build information for using the current method; the tool-data/shared/ensembl/ensembl_sites_data_URL.txt file has the site and build information for when the older method is to be used.
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The new method follows: http://www.ensembl.org/info/docs/webcode/linking.html
The old method follows: http://aug2007.archive.ensembl.org/Homo_sapiens/helpview?se=1;kw=urlsource
2010-05-21 15:25:56 -04:00
Jeremy Goecks
7e0b4e88fb
Enable display framework to handle unicode characters in item titles and enable pages to have unicode characters in titles.
2010-05-21 14:41:20 -04:00
Ross Lazarus
e7243bacf2
Unreverted js changes from JG - for some strange reason they break the tool upload form here although functional tests seem fine
2010-05-21 13:43:50 -04:00
Nate Coraor
d8281a6e77
add multiprocess.sh example script for running multiple galaxy processes. instructions coming later.
2010-05-20 17:00:12 -04:00
Ramkrishna Chakrabarty
35236266b8
added more options to the sff converter tool
2010-05-20 15:36:07 -04:00
Ross Lazarus
d61fd8c4df
Added ldindep datatype to datatypes sample
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Added snpwga tool sections to tool_conf.sample.main - need these
2010-05-20 14:16:08 -04:00
Ross Lazarus
72887358d3
Once more with even more feeling - welcome.html restored restored
2010-05-20 14:10:39 -04:00
Ross Lazarus
cd4d176ca7
eeesh. hgignore for welcome.html didn't
2010-05-20 14:07:10 -04:00
Ross Lazarus
bf9b651afa
Removed redundant code from rgEigPCA.py now that it takes a pre-converted ldindep dataset.
2010-05-20 12:41:51 -04:00
Ross Lazarus
d4ebd35d3a
More tweaks to some snp/wga composite output test comparisons - all png/pdf should be sim_size rather than lines_diff
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Updated test outputs for snp/wga tools
Testing a new hgignore so welcome.html should not be overwritten
2010-05-20 12:38:35 -04:00
Ross Lazarus
dae39752f0
Added ldIndep datatype to genetics.py and datatypes_conf for ld reduced datasets - these are pbed
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files that have had one of each pair of redundant SNP in high LD with each other removed for GRR and ancestry PCA
where the redundancy adds no additional information but slows things down
Added converter for pbed to ldindep to converters and to datatypes_conf
Adjusted rgGRR and rgEigPCA tools to use these
2010-05-19 10:28:41 -04:00
Jeremy Goecks
c81b275d1c
Replace big selects that refresh on change with search+select.
2010-05-17 10:58:16 -04:00
Jeremy Goecks
3b0e98e4cb
Better UI flow for changing an HDA's data type.
2010-05-15 13:12:38 -04:00
Jeremy Goecks
23829acc7b
Enable images and binary datasets to work within the display framework. More work is needed to enable images to work well.
2010-05-15 11:25:05 -04:00
Greg Von Kuster
a65852ca60
Fixes for editing tool information and submitting a tool for approval in the community space.
2010-05-14 11:25:03 -04:00
Nate Coraor
e4055bfb6b
Use PBS exit_status (if keep_completed is set) so we can detect PBS failures.
2010-05-14 10:37:36 -04:00
Jeremy Goecks
9a4e703f51
Fix comment.
2010-05-14 10:19:12 -04:00
Jeremy Goecks
b2fedd981c
Add GFF filtering tool. Tool filters GFF file based on an attribute value.
2010-05-14 10:15:48 -04:00
Jeremy Goecks
ab8e750624
Add track definition to bedgraph files generated by gtf2bedgraph.
2010-05-13 15:35:41 -04:00
Greg Von Kuster
0de5b667f9
Fix for editing category information in the community space.
2010-05-13 14:10:37 -04:00
Jeremy Goecks
08e6cee1fc
Only use search+select when jquery autocomplete plugin is defined.
2010-05-13 12:14:52 -04:00
Dannon Baker
bfcb63b35e
Fix for issue where connecting to a Workflow Step that had been changed wasn't being saved
2010-05-13 12:03:17 -04:00
Greg Von Kuster
66463eb6e9
Fix for changing a library dataset's data type ( resolves ticket # 333 ), add the library dataset's data type to the library dataset info page, and add <pre> tags to the tool description on the tool information page in the community space.
2010-05-13 09:35:57 -04:00
Kanwei Li
d815c09491
trackster:
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- Prompt when leaving a viz with unsaved changes
- Can only add datatypes of the same dbkey
2010-05-12 17:43:29 -04:00
Daniel Blankenberg
64c68b5a66
Several Fixes for Uploading Composite datatypes. Revert changeset 3769:69e70e588a8e.
2010-05-12 15:57:05 -04:00
Greg Von Kuster
95ac03c352
Remove the hack I just committed for changing modENCODE fly and worm dbkeys, and translate the values in the tool configs.
2010-05-12 15:18:40 -04:00
Greg Von Kuster
de5de2973c
Force modENCODE worm dbkey to be ce6 and modENCODE fly dbkey to be dm2.
2010-05-12 14:50:25 -04:00
Greg Von Kuster
3eef17415b
Fixes for displaying appropriate datasets in GBrowse wormbase, modENCODE worm, and modENCODE fly.
2010-05-12 14:37:00 -04:00
Nate Coraor
89849e12ce
Fix buildbot's builds.txt
2010-05-12 11:43:57 -04:00
Jeremy Goecks
a5f839538e
Enable viewing of datasets via history/view when user is not logged in and/or when user does not have public username.
2010-05-12 09:51:31 -04:00
Greg Von Kuster
cea2ff14ef
Fixes for uploading a tool to the community space, and keep None from being displayed if there is no user_description.
2010-05-12 09:18:05 -04:00
Ross Lazarus
01b583e0fe
work around for composite objects without a base_name in grouping.py
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removed artefacts from Manhattan plot example in the rgManQQ tool help
2010-05-11 18:02:39 -04:00
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
Daniel Blankenberg