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https://github.com/genome/genome
23 March 2024, 19:04:16 UTC
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Revision Author Date Message Commit Date
d8b1051 Thomas Mooney 30 March 2015, 17:09:11 UTC Whitespace. 30 March 2015, 17:09:11 UTC
a66b151 Susanna Siebert 30 March 2015, 15:08:35 UTC Make a class for merged AlignedBamResults and use it where appropriate 30 March 2015, 15:40:57 UTC
de88b05 Dave Larson 30 March 2015, 15:12:52 UTC change default version of G::M::T::Sam::Readcount to use bam-readcount v0.7 30 March 2015, 15:12:52 UTC
06d184c Nathaniel Nutter 28 March 2015, 18:09:22 UTC Merge pull request #596 from nnutter/master use canonpath to normalize $test_dir 28 March 2015, 18:09:22 UTC
f5dde25 Nathaniel Nutter 27 March 2015, 22:11:22 UTC use canonpath to normalize $test_dir Use canonpath to normalize path as something in StreamGraph seemed to do the same. For example, `./WorkflowBuilder` becomes just `WorkflowBuilder` which was breaking the full test suite. 27 March 2015, 22:11:22 UTC
17421ed Allison Penner Regier 27 March 2015, 18:32:03 UTC Merge pull request #593 from apregier/shortcut_adaptor Add shortcut to adaptor class 27 March 2015, 18:32:03 UTC
f09043c apregier 27 March 2015, 17:54:11 UTC Shortcut delegates to execute 27 March 2015, 17:54:11 UTC
1c156a1 Susanna Siebert 27 March 2015, 14:36:53 UTC Make MarkDuplicates a G::M::T::Picard::Base 27 March 2015, 14:36:53 UTC
f713990 Susanna Siebert 27 March 2015, 14:36:23 UTC Fix picard class names 27 March 2015, 14:36:23 UTC
9a3dc91 Susanna Siebert 27 March 2015, 14:35:40 UTC Consolidate recent Picard changes 27 March 2015, 14:35:40 UTC
c44ea31 Allison Penner Regier 27 March 2015, 14:34:09 UTC Merge pull request #546 from apregier/compare_vcf_in_process Compare vcf in process 27 March 2015, 14:34:09 UTC
2679d82 Susanna Siebert 27 March 2015, 14:33:08 UTC Put text fields in quotes 27 March 2015, 14:33:08 UTC
bfe3ddb apregier 27 March 2015, 01:37:22 UTC Add shortcut to adaptor class There is no reason why this should ever need to run with lots of resources 27 March 2015, 01:38:22 UTC
eab32f6 Thomas B. Mooney 26 March 2015, 21:37:33 UTC Merge pull request #586 from tmooney/remove_unused_properties_from_composite_workflow Remove disused properties. 26 March 2015, 21:37:33 UTC
76f1a76 Thomas B. Mooney 26 March 2015, 21:37:15 UTC Merge pull request #585 from tmooney/dont_log_rollbacks_on_build_requested Don't log rollbacks on build requested 26 March 2015, 21:37:15 UTC
098ef67 Susanna Siebert 26 March 2015, 20:57:30 UTC Merge remote-tracking branch 'origin/master' into qc_framework 26 March 2015, 20:57:30 UTC
6900b8f Susanna Siebert 26 March 2015, 20:56:03 UTC Merge remote-tracking branch 'origin/master' into qc_framework 26 March 2015, 20:56:03 UTC
5ccc6a2 Ian Ferguson 26 March 2015, 20:55:18 UTC Merge pull request #573 from iferguson90/picard-class-fix Picard classnames 26 March 2015, 20:55:18 UTC
df7702f Eddie Belter 26 March 2015, 19:41:21 UTC Merge pull request #590 from ebelter/instdata2 InstData Import: give default value to resolved instdata properties 26 March 2015, 19:41:21 UTC
2352f4c Eddie Belter 26 March 2015, 19:40:57 UTC Merge pull request #584 from ebelter/instdata-description InstData Import: pass description on to created instdasta 26 March 2015, 19:40:57 UTC
a828d62 apregier 26 March 2015, 19:39:08 UTC Simplify by passing arguments straight through 26 March 2015, 19:39:08 UTC
ab60abc Nathaniel Nutter 26 March 2015, 19:37:44 UTC Merge pull request #591 from nnutter/master make StreamGraph.t independent of current working directory 26 March 2015, 19:37:44 UTC
8b314a0 Avinash Ramu 26 March 2015, 19:27:44 UTC Merge pull request #547 from gatoravi/clinseq_update_analysis clinseq: update defaults in update-analysis 26 March 2015, 19:27:44 UTC
cdbf64b Ian Ferguson 26 March 2015, 18:48:32 UTC Use an HTTP request instead of a socket 26 March 2015, 18:48:32 UTC
9ab9c24 Avinash Ramu 26 March 2015, 16:27:35 UTC pull in snapshot changes from master 26 March 2015, 16:27:35 UTC
801ac9d Susanna Siebert 26 March 2015, 15:51:58 UTC Fix package name for MarkDuplicates in Picard 1.123 26 March 2015, 15:51:58 UTC
46a7998 Avinash Ramu 26 March 2015, 15:36:17 UTC Merge remote-tracking branch 'origin' into clinseq_update_analysis 26 March 2015, 15:36:17 UTC
e34a533 Avinash Ramu 26 March 2015, 15:33:39 UTC update db snapshot 26 March 2015, 15:33:39 UTC
ad3ab9b Thomas Mooney 26 March 2015, 13:29:14 UTC Replace caller with Carp::shortmess. 26 March 2015, 13:29:14 UTC
edc004b APipe Tester 26 March 2015, 12:16:55 UTC Updated `genome` tab completion. 26 March 2015, 12:16:55 UTC
66f9153 APipe Tester 26 March 2015, 12:15:07 UTC Updated class browser cache. 26 March 2015, 12:15:07 UTC
05f3b91 Ian Ferguson 25 March 2015, 20:17:42 UTC Collect call info and send it to my workstation 25 March 2015, 20:17:42 UTC
0b9c64d Ian Ferguson 25 March 2015, 19:57:14 UTC Don't die when supplied with an undef Picard vers. 25 March 2015, 19:57:14 UTC
1393ae4 Nathaniel Nutter 25 March 2015, 19:30:21 UTC make StreamGraph.t independent of current working directory 25 March 2015, 19:30:21 UTC
ea96bf9 Eddie Belter 25 March 2015, 18:30:35 UTC InstData Import: give default value to resolved instdata properties 25 March 2015, 18:30:35 UTC
c3b5255 Eddie Belter 25 March 2015, 17:13:02 UTC InstData Import: spell cprrect 25 March 2015, 17:13:02 UTC
d2781f2 Susanna Siebert 25 March 2015, 17:10:57 UTC Merge pull request #587 from susannasiebert/alignment_result Filter out G::ID::AlignmentResult 25 March 2015, 17:10:57 UTC
cb14972 Thomas B. Mooney 25 March 2015, 17:00:04 UTC Merge pull request #581 from tmooney/optional_tag_during_add_menu_item Optionally add tag(s) when associating menu item(s) to the AnP. 25 March 2015, 17:00:04 UTC
25330bf apregier 24 March 2015, 21:12:19 UTC Update blessed process 25 March 2015, 16:18:38 UTC
ece26e1 apregier 24 March 2015, 21:11:46 UTC Properly print out NA if no error rate available 25 March 2015, 16:18:38 UTC
9497996 Susanna Siebert 05 March 2015, 17:08:49 UTC updated the blessed trio process 25 March 2015, 16:18:38 UTC
edf862d apregier 25 February 2015, 21:44:28 UTC Imported instrument data doesn't have filt_error_rate_avg 25 March 2015, 16:18:37 UTC
66573dd apregier 25 February 2015, 19:41:58 UTC Need to put ids in yaml file 25 March 2015, 16:18:37 UTC
eaf31ff apregier 25 February 2015, 15:29:41 UTC Fix yaml formatting 25 March 2015, 16:05:07 UTC
339e06f apregier 25 February 2015, 15:29:24 UTC Small fixes 25 March 2015, 16:05:07 UTC
45e75da Susanna Siebert 24 February 2015, 20:34:58 UTC add module to parse process test yaml 25 March 2015, 16:05:07 UTC
3f560c5 Susanna Siebert 25 March 2015, 14:19:12 UTC Remove breakpoint 25 March 2015, 14:19:12 UTC
7ebe5b9 Susanna Siebert 25 March 2015, 14:18:14 UTC Move Picard-specific cmd_line subroutine to Picard.pm 25 March 2015, 14:18:14 UTC
091467d Susanna Siebert 25 March 2015, 14:16:00 UTC Use temp file path instead of __FILE__ 25 March 2015, 14:16:00 UTC
3017e52 Susanna Siebert 25 March 2015, 13:41:30 UTC Filter out G::ID::AlignmentResult Since per-lane alignments are now G::ID::AlignedBamResult they need to be explicitly filtered out 25 March 2015, 13:41:30 UTC
a9a456b Thomas B. Mooney 25 March 2015, 13:29:12 UTC Merge pull request #579 from tmooney/merge_error_message_on_deleted_object Don't call error_message on a deleted object. 25 March 2015, 13:29:12 UTC
321cd84 Thomas Mooney 25 March 2015, 13:26:52 UTC Remove disused properties. 25 March 2015, 13:26:52 UTC
ea3c493 Thomas Mooney 25 March 2015, 13:09:25 UTC Remove old comments. * We already do have a note. * This isn't especially TGI-specific. 25 March 2015, 13:09:25 UTC
e941937 Thomas Mooney 25 March 2015, 13:04:16 UTC Remove the caller check; make the "real" property _build_requested 25 March 2015, 13:04:16 UTC
ca7d3e5 Thomas Mooney 24 March 2015, 23:06:08 UTC Test that QC decorator modifies workflow properly. 24 March 2015, 23:06:08 UTC
a3d938b Thomas Mooney 24 March 2015, 22:45:48 UTC Basic test for decorator delegation. 24 March 2015, 22:49:06 UTC
a6a8363 Thomas Mooney 11 March 2015, 21:38:16 UTC Add a test of decorators. 24 March 2015, 22:30:01 UTC
b022316 Thomas Mooney 11 March 2015, 21:37:17 UTC Extract _test_strategy to perform the create/execute/diff cycle. 24 March 2015, 22:30:01 UTC
3399449 Thomas Mooney 11 March 2015, 21:35:49 UTC Create $package variable for easier reuse. 24 March 2015, 22:30:01 UTC
2be018e Thomas B. Mooney 24 March 2015, 22:02:39 UTC Merge pull request #577 from tmooney/more_consistent_bases_warnings Don't Warn about Each Missing ".bases" File if We Didn't Make Any 24 March 2015, 22:02:39 UTC
97fbed8 Thomas Mooney 24 March 2015, 21:39:46 UTC Also unlock if our change was rolled back. 24 March 2015, 21:39:46 UTC
b7ce6a3 Thomas Mooney 24 March 2015, 21:38:24 UTC When rolling back, don't lock or record a note. * We don't need to lock, since we're not changing the value. * We don't need to record a note, since the note of the original change will be removed. 24 March 2015, 21:38:24 UTC
47caba6 apregier 24 March 2015, 20:39:50 UTC igv xml file has urls that will be different for each run 24 March 2015, 20:39:50 UTC
3ef7af6 Eddie Belter 24 March 2015, 20:16:38 UTC InstData Import: pass description on to created instdasta 24 March 2015, 20:16:38 UTC
b6ceff1 APipe Tester 24 March 2015, 19:19:53 UTC updated workflow submodule to 0b9e071 24 March 2015, 19:19:53 UTC
ecffc88 Thomas Mooney 23 March 2015, 14:35:41 UTC Override QC in the test so we don't really try to run it. 24 March 2015, 19:19:34 UTC
4895569 Thomas Mooney 23 March 2015, 14:25:58 UTC Provide a way to programmatically pass the users hash. 24 March 2015, 19:19:33 UTC
4efdf7e Ian Ferguson 24 March 2015, 19:15:34 UTC Add Picard version to Bwamem.t 24 March 2015, 19:15:34 UTC
afb33c8 Ian Ferguson 24 March 2015, 19:03:43 UTC Die when explicitly given an undef Picard version 24 March 2015, 19:03:43 UTC
26e5059 Thomas Mooney 23 March 2015, 22:17:29 UTC Stop using GENOME_LSF_QUEUE_ALIGNMENT_PROD. * Since the queues are controlled by environment variables, the user can select between the multiple alignment queues by controlling their environment. * Leave the old environment variable in as non-required for now (so as to not break everyone's configurations when we deploy the new snapshot). 24 March 2015, 17:56:35 UTC
284f752 Susanna Siebert 24 March 2015, 17:07:39 UTC Another typo fix 24 March 2015, 17:07:39 UTC
f1d20a8 Susanna Siebert 24 March 2015, 17:06:36 UTC Fix typo 24 March 2015, 17:06:36 UTC
cad4a6e Susanna Siebert 24 March 2015, 17:01:01 UTC Override nondeterministic subroutine 24 March 2015, 17:01:01 UTC
b045a2c APipe Tester 24 March 2015, 16:25:08 UTC updated workflow submodule to 297de2d 24 March 2015, 16:25:08 UTC
c7abe9c Thomas Mooney 19 March 2015, 21:57:35 UTC Add testcase for QC decorator. 24 March 2015, 16:12:29 UTC
27af3ad Thomas Mooney 19 March 2015, 20:59:12 UTC A QC decorator. 24 March 2015, 16:12:29 UTC
8bbe0ee Thomas Mooney 19 March 2015, 20:37:49 UTC Process decorations (if any). 24 March 2015, 16:12:28 UTC
45694e1 Thomas Mooney 11 March 2015, 20:16:46 UTC Also make the result available as an output. 24 March 2015, 16:12:28 UTC
215e9ee Thomas Mooney 10 March 2015, 19:21:53 UTC Add factory and base class for decorators. 24 March 2015, 16:12:26 UTC
5e3e655 Thomas Mooney 10 March 2015, 19:16:18 UTC Add optional decorators to alignment strategy 24 March 2015, 16:12:25 UTC
b35517b Susanna Siebert 23 March 2015, 20:20:02 UTC Enforce minimum Picard version 24 March 2015, 16:00:00 UTC
6ab3dcf Susanna Siebert 23 March 2015, 20:07:51 UTC New qc tool for Picard CollectWgsMetrics 24 March 2015, 16:00:00 UTC
cc709e6 Susanna Siebert 23 March 2015, 20:07:30 UTC New wrapper for Picard CollectWgsMetrics 24 March 2015, 16:00:00 UTC
668723c Susanna Siebert 18 March 2015, 21:34:53 UTC Implement MarkDuplicates qc tool and tests 24 March 2015, 16:00:00 UTC
29a6fbf Susanna Siebert 18 March 2015, 21:34:00 UTC Implement CollectGcBiasMetrics qc tool and tests 24 March 2015, 15:59:59 UTC
2d12fdb Susanna Siebert 18 March 2015, 21:33:29 UTC Implement CalculateHsMetrics qc tool and tests 24 March 2015, 15:59:59 UTC
95c9cf9 Susanna Siebert 18 March 2015, 21:33:00 UTC Finish implementation of CollectMultipleMetrics qc tool and add tests 24 March 2015, 15:59:59 UTC
00b9c95 Susanna Siebert 18 March 2015, 21:12:43 UTC Fix erroneous shift 24 March 2015, 15:59:59 UTC
2db2608 Susanna Siebert 18 March 2015, 21:10:10 UTC Fix package name for version 1.122 and up 24 March 2015, 15:59:59 UTC
fffcc40 Susanna Siebert 18 March 2015, 21:09:35 UTC Split out command line creation into build_cmdline_string and build_cmdline_list for qc compatibility 24 March 2015, 15:59:59 UTC
0002e49 Susanna Siebert 18 March 2015, 15:59:49 UTC Framework for metrics parsing of Picard output 24 March 2015, 15:59:59 UTC
932400a Susanna Siebert 18 March 2015, 15:54:12 UTC Some tweaks to qc metrics processing 24 March 2015, 15:59:59 UTC
31deecf Susanna Siebert 17 March 2015, 19:02:46 UTC Create command that returns command line as list 24 March 2015, 15:59:59 UTC
d41fad9 Susanna Siebert 16 March 2015, 15:14:53 UTC Make a parent class for Picard qc tools 24 March 2015, 15:59:58 UTC
2cdbdd0 Susanna Siebert 24 March 2015, 15:59:02 UTC Merge pull request #576 from susannasiebert/alignment_result Make AlignmentResult an AlignedBamResult 24 March 2015, 15:59:02 UTC
328aa5d Allison Penner Regier 24 March 2015, 15:51:52 UTC Merge pull request #556 from apregier/qc_framework Qc framework 24 March 2015, 15:51:52 UTC
d2fa606 Thomas Mooney 24 March 2015, 14:09:16 UTC Optionally add tag(s) when associating menu item(s) to the AnP. 24 March 2015, 14:09:16 UTC
2fdc12b Susanna Siebert 24 March 2015, 13:18:12 UTC use skip blog instead of commenting out test 24 March 2015, 13:18:12 UTC
4831163 Thomas Mooney 24 March 2015, 13:09:28 UTC Don't call error_message on a deleted object. The rollback will have rolled back our creation. 24 March 2015, 13:09:28 UTC
cbe7dfe Thomas Mooney 23 March 2015, 20:52:11 UTC Create the manifest file before the final reallocation. 23 March 2015, 20:52:11 UTC
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