Nate Coraor
b8fd7dbe2e
Add Picard and fastqc tools to Main
2011-05-19 10:07:53 -04:00
Jeremy Goecks
41446bb4b0
Merge.
2011-05-18 16:52:38 -04:00
Jeremy Goecks
c6797482af
Remove obsolete test values for Cufflinks and Cuffdiff tests.
2011-05-18 16:52:14 -04:00
Kelly Vincent
ac95877120
merge
2011-05-18 16:51:51 -04:00
Kelly Vincent
6308d93385
Further tweaks to Picard help text
2011-05-18 16:50:37 -04:00
Jeremy Goecks
8db5b83322
Clone annotation and tags when cloning workflows.
2011-05-18 16:48:02 -04:00
Kelly Vincent
804f9ab60a
Cleaned up help text across Picard tools (and FastQC) to standardize style as much as possible
2011-05-17 21:31:34 -04:00
Kanwei Li
d340c2ab22
Fix data.py typo. Fixes #543
2011-05-17 18:41:12 -04:00
Ross Lazarus
c600bed50c
grr - more vanity attribution removed
2011-05-17 13:14:15 -04:00
Ross Lazarus
5096aec964
cleaned up picard tool names - own section so (picard) was redundant
2011-05-17 13:04:35 -04:00
Ross Lazarus
e0545fcd8f
separated ngs picard tools and removed fastqc wrapper lgpl annotation
2011-05-17 12:52:24 -04:00
Ross Lazarus
e5a2a48285
branch merge with Kelly's fixes
2011-05-17 12:14:32 -04:00
Daniel Blankenberg
1dfdc42fe6
Update tool help for some MAF tools.
2011-05-17 12:07:25 -04:00
Kelly Vincent
778088bba9
Modified Tophat wrapper so dbkey will be properly set both for built-in and history references
2011-05-17 12:05:07 -04:00
Ross Lazarus
0aa96d8f0f
branch merge
2011-05-17 11:39:52 -04:00
Jeremy Goecks
2b7025f11d
Enable Cufflinks to work when setting metadata externally.
2011-05-17 11:21:26 -04:00
Ross Lazarus
2e286b5c2d
amerkinized spelin' and removed copyright notices on some picard tool forms
2011-05-17 10:29:06 -04:00
Kelly Vincent
7401ae6439
Numerous updates to Picard tools: Cleaned up and standardized wrapper's Python code, removing redundant variables and using the same ones in different segment of code when possible; Changed sam/bam outputs to be bam by default and use change_format if user requests sam and removed redundant output parameters; Got tests passing for AddOrReplaceReadGroups; Relaxed the matching constraints for output for BamIndexStats and InsertSize wrappers Standardized on the parameter output-format rather than newformat to indicate sam preference over bam
2011-05-17 01:57:04 -04:00
Kanwei Li
5caf51ddaa
trackster: Refactor LineTrack overflow, fix it to work better for Line and Filled modes
2011-05-16 17:08:06 -04:00
Ross Lazarus
6dcd6433e3
removed python2.4 from rgfakePed.py
2011-05-16 10:03:47 -04:00
Ross Lazarus
fa23935ae5
repairs to rgfakePed tool for generating null genotype data - since removing the _code.py trick of renaming composite file components means all of the parts (eg map and ped) acquire the default name of RgeneticsData, that's what the tool has to create - rather than sensibly named components based on the title - since only way to fix this wart is to reintroduce a bigger wart using the post execution hook, decided to just go with that default base_name to make things more sustanable in the long term
2011-05-16 09:12:19 -04:00
Ross Lazarus
7859f56954
reverting reorder test outputs - PhiX reference used to generate them seems different from that on the buildbot
2011-05-13 21:24:03 -04:00
Ross Lazarus
d5fbb00c33
picard wrapper typo fixed
2011-05-13 20:46:38 -04:00
Ross Lazarus
04d6cd3563
branch merge
2011-05-13 17:12:44 -04:00
Ross Lazarus
5e25812f6f
finally have picard reorder tests working
2011-05-13 17:12:19 -04:00
Ross Lazarus
26eaf7a853
Picard reorder test fix and parameter changes
2011-05-13 16:54:31 -04:00
Kanwei Li
3275e4558c
trackster: tweak resolution, fix LineTrack data bug
2011-05-13 16:49:43 -04:00
Ross Lazarus
dfeeecdff8
Reordersam fails silently if contig names do not match so added an html log where this can be seen easily. Updated insertsize test
2011-05-13 15:23:32 -04:00
Jeremy Goecks
649bd62af7
Trackster: enable chaining of filters.
2011-05-13 10:02:28 -04:00
Ross Lazarus
51c28a1a51
branch merge
2011-05-13 08:32:35 -04:00
Jeremy Goecks
4476d5eb00
Trackster: reset filters when they are hidden.
2011-05-12 20:01:42 -04:00
Jeremy Goecks
3eb0c50ae4
Trackster: enable dynamic filters to be run on complete dataset using filter tools.
2011-05-12 17:12:01 -04:00
Ross Lazarus
ecaafc3dff
more fixes for tests related to new logging method for picard tools
2011-05-12 16:53:11 -04:00
Ross Lazarus
75bb1c585f
branch merge
2011-05-12 16:48:45 -04:00
Ross Lazarus
e62a43a621
update some test outputs for picard
2011-05-12 16:48:31 -04:00
Kelly Vincent
c565726192
Updated help section of BWA wrappers to include tags for the RG header record type
2011-05-12 13:38:00 -04:00
Daniel Blankenberg
d69fe3360f
Add GATK tool-data to buildbot_setup.sh links.
2011-05-12 12:20:52 -04:00
Daniel Blankenberg
7b6ee414f0
Have GATK file listings written as html, be sorted.
2011-05-12 12:13:18 -04:00
Nate Coraor
f61df55b8f
Fix test output for picard_ARRG.
2011-05-12 11:55:32 -04:00
Nate Coraor
a7f17d327d
Add a method to add manual builds to buildbot runs.
2011-05-12 11:53:32 -04:00
Ross Lazarus
26b865685c
Picard wrapper modified to use python logging module for all logging
2011-05-12 09:56:01 -04:00
Daniel Blankenberg
5022609ecb
Allow gatk_wrapper.py to run in versions of python<2.6.
2011-05-11 16:02:06 -04:00
Kanwei Li
efe0cba6d8
trackster: Fix border and error not lining up at right place
2011-05-11 15:43:33 -04:00
Jeremy Goecks
01ec149d82
Add support for comment handling to gff_to_interval_index tool.
2011-05-11 15:38:57 -04:00
Jeremy Goecks
9cfeed2961
Relax diff calculation for Cuffdiff test to account for non-deterministic output.
2011-05-11 15:07:24 -04:00
Kanwei Li
a706fc3796
Show details: now works even when tool is obsolete. Show inheritance chain where the dataset came from if it was copied from a history or library
2011-05-11 11:36:22 -04:00
Kelly Vincent
9eaf2ec821
Updated SRMA to properly set dbkey and changed functional tests so that they can handle a single line difference for the SRMA version number tag
2011-05-11 10:49:32 -04:00
Daniel Blankenberg
b2ad8233db
Some minor fixes for 5537:1a379a0f2ecc.
2011-05-11 10:46:46 -04:00
Daniel Blankenberg
364180ef7d
First pass at adding some GATK tools. Included tools are "Realigner Target Creator", "Indel Realigner", "Count Covariates", "Table Recalibration", "Analyze Covariates" and "Unified Genotyper". These tool integrations should be considered beta: changes that will not be backwards-compatible with workflows and re-run functionality should be expected.
...
TODO:
A few new datatypes have been declared, but exist in name only (subclasses of Text defined only in datatypes_conf.xml), these should be refined to be true datatypes, with proper peeks, sniffing, metadata, etc.
Help sections need work.
HTML listing of files in e.g. Analyze Covariates should be prettified.
Other items not listed.
2011-05-11 09:38:23 -04:00
Daniel Blankenberg
3cbead3137
Add a "contains" compare type to functional tests. Enables simple checking for substrings in a test output file, on a line-by-line basis. TODO: Enhance to enforce order.
2011-05-10 20:11:52 -04:00
Nate Coraor