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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
3058b6c APipe Tester 19 October 2016, 12:17:32 UTC Updated `genome` tab completion. 19 October 2016, 12:17:32 UTC
0a04c8a APipe Tester 19 October 2016, 12:16:11 UTC Updated class browser cache. 19 October 2016, 12:16:11 UTC
18c748d Susanna Kiwala 18 October 2016, 21:11:44 UTC Deduplicate snv_indel_report subroutines 18 October 2016, 21:20:00 UTC
90cc583 Susanna Kiwala 18 October 2016, 20:13:54 UTC Also look for the snv_indel_report_clean_unfiltered_file and snv_indel_report_clean_filtered_file by the subject's name 18 October 2016, 20:16:41 UTC
4e67567 Feiyu Du 18 October 2016, 19:48:15 UTC Merge pull request #1594 from dufeiyu/pass_detailed Add detailed.pass.vcf to DV2 output 18 October 2016, 19:48:15 UTC
9da2d18 Thomas B. Mooney 18 October 2016, 19:35:19 UTC Remove old build workflow configuration. 18 October 2016, 19:35:19 UTC
05dcd80 Feiyu Du 13 October 2016, 18:26:34 UTC print warning message if output file is not compressed for tabix 13 October 2016, 18:26:34 UTC
afcdebb Feiyu Du 13 October 2016, 16:47:30 UTC Merge pull request #1595 from dufeiyu/cle_test Update blessed process for CLE test 13 October 2016, 16:47:30 UTC
74a2855 Feiyu Du 13 October 2016, 15:34:46 UTC Update blessed process for CLE test 13 October 2016, 15:34:46 UTC
d898451 APipe Tester 13 October 2016, 12:15:11 UTC Updated `genome` tab completion. 13 October 2016, 12:15:11 UTC
d85bb6e APipe Tester 13 October 2016, 12:13:47 UTC Updated class browser cache. 13 October 2016, 12:13:47 UTC
c520d80 Thomas B. Mooney 12 October 2016, 22:24:10 UTC Merge pull request #1559 from tmooney/retire_workflow Remove support for "Workflow". 12 October 2016, 22:24:10 UTC
606e610 Feiyu Du 12 October 2016, 19:20:49 UTC for some cases without filters, detecotr vcf is used without FT in format field 12 October 2016, 19:20:49 UTC
41d877f Feiyu Du 12 October 2016, 17:00:35 UTC add methods to get detailed.pass vcf 12 October 2016, 17:00:35 UTC
bae7dce Feiyu Du 12 October 2016, 16:59:30 UTC add step to make detailed_pass vcf 12 October 2016, 16:59:30 UTC
a8f06d2 Feiyu Du 11 October 2016, 18:00:00 UTC Add FinalPassOnly and its unit test 11 October 2016, 18:00:00 UTC
c858c0b Feiyu Du 06 October 2016, 21:15:27 UTC Merge pull request #1592 from dufeiyu/bless Bless new build for apipe-test-somatic-variation 06 October 2016, 21:15:27 UTC
dfa9496 Feiyu Du 06 October 2016, 19:28:14 UTC bless new build for apipe-test-somatic-variation 06 October 2016, 19:28:14 UTC
7295d49 Jason Walker 04 October 2016, 18:33:15 UTC add AnP name to the report summary. 04 October 2016, 18:33:15 UTC
c915685 Feiyu Du 03 October 2016, 19:28:37 UTC Merge pull request #1589 from dufeiyu/testDB_update Update test database 03 October 2016, 19:28:37 UTC
eea04c9 Feiyu Du 03 October 2016, 15:10:22 UTC update test database 03 October 2016, 15:10:22 UTC
b06f70c Feiyu Du 03 October 2016, 15:04:36 UTC Add test for current homo_polymer list in use 03 October 2016, 15:04:36 UTC
a8c7b6b Susanna Kiwala 03 October 2016, 13:53:45 UTC Make sure the $tumor_subject_common_name is defined before regexing it 03 October 2016, 13:53:45 UTC
ed83e60 Thomas B. Mooney 29 September 2016, 20:51:07 UTC Remove "email_pipeline_noisy" config. There was only one place left using this, and it already sends mail somewhere else in addition to this configured address. 29 September 2016, 20:51:07 UTC
7aa370e Feiyu Du 29 September 2016, 01:01:30 UTC Merge pull request #1586 from dufeiyu/update_trio_process Update blessed process object for Jenkins genome-process-test 29 September 2016, 01:01:30 UTC
715bc39 Feiyu Du 28 September 2016, 20:52:37 UTC update blessed process 28 September 2016, 20:52:37 UTC
5f43026 Feiyu Du 28 September 2016, 18:17:02 UTC Merge pull request #1584 from dufeiyu/format_index Reset _format_key_to_idx hash properly and avoid check with autovivified hash 28 September 2016, 18:17:02 UTC
2c6ed31 Thomas B. Mooney 28 September 2016, 15:50:49 UTC Merge pull request #1580 from tmooney/snv_indel_report_requests_tmp Request some temp space for the SnvIndelReport step. 28 September 2016, 15:50:49 UTC
7636446 Feiyu Du 27 September 2016, 21:57:52 UTC Make changes based on review feedback 27 September 2016, 21:57:52 UTC
3f18ace Dave Larson 27 September 2016, 21:09:43 UTC Merge pull request #1585 from ernfrid/master Fix flagstat tests 27 September 2016, 21:09:43 UTC
01156fa Feiyu Du 27 September 2016, 20:27:39 UTC fix Expert.t 27 September 2016, 20:27:39 UTC
f83d8b4 Feiyu Du 27 September 2016, 19:54:22 UTC fix AnnotateWithReadcounts.t 27 September 2016, 19:54:22 UTC
612d959 Dave Larson 27 September 2016, 16:57:15 UTC fix tests. doh! 27 September 2016, 16:57:15 UTC
7a88ccb Dave Larson 27 September 2016, 16:39:11 UTC Merge pull request #1583 from ernfrid/fix_interchromosomal_calc change denominator for interchromosomal rate calculation 27 September 2016, 16:39:11 UTC
eb0b306 Feiyu Du 27 September 2016, 16:24:22 UTC add to unit test 27 September 2016, 16:24:22 UTC
4190850 Feiyu Du 27 September 2016, 16:23:01 UTC Use solid hash check, _format_key_to_idx hash can be autovivified 27 September 2016, 16:23:01 UTC
5bb7060 Feiyu Du 27 September 2016, 16:18:10 UTC Reset _format_key_to_idx properly 27 September 2016, 16:18:10 UTC
b9691e8 Dave Larson 26 September 2016, 15:10:13 UTC change denominator for interchromosomal rate calculation 26 September 2016, 15:10:13 UTC
7ff6b6b APipe Tester 22 September 2016, 12:18:45 UTC Updated `gmt` tab completion. 22 September 2016, 12:18:45 UTC
cf6c114 APipe Tester 22 September 2016, 12:18:06 UTC Updated `genome` tab completion. 22 September 2016, 12:18:06 UTC
ce39960 APipe Tester 22 September 2016, 12:16:39 UTC Updated class browser cache. 22 September 2016, 12:16:39 UTC
f33863e Feiyu Du 21 September 2016, 21:10:35 UTC Merge pull request #1576 from dufeiyu/homo_polymer Update homo_polymer list with min_length 7 21 September 2016, 21:10:35 UTC
49fc153 Thomas B. Mooney 21 September 2016, 19:51:45 UTC Request some temp space for the SnvIndelReport step. 21 September 2016, 19:51:45 UTC
1209fdc Thomas B. Mooney 21 September 2016, 19:02:45 UTC Merge pull request #1579 from tmooney/remove_denovo_soap Remove `gmt soap` tree and disable Soap alignment results. 21 September 2016, 19:02:45 UTC
a8a3912 Thomas B. Mooney 21 September 2016, 18:24:20 UTC Remove `gmt soap` tree and disable Soap alignment results. 21 September 2016, 18:44:48 UTC
ba12ccd Thomas B. Mooney 21 September 2016, 18:38:43 UTC Merge pull request #1578 from tmooney/breakdancer_test_doesnt_depend_on_path Make Breakdancer test independent of test data location. 21 September 2016, 18:38:43 UTC
6164456 Thomas B. Mooney 21 September 2016, 17:59:41 UTC Use File::Spec->join. 21 September 2016, 17:59:41 UTC
030bd10 Thomas B. Mooney 21 September 2016, 17:52:45 UTC Process the Breakdancer config to point to the current directory. 21 September 2016, 17:53:34 UTC
b7120c0 Thomas B. Mooney 21 September 2016, 17:34:47 UTC Ignore absolute file paths when comparing output. 21 September 2016, 17:34:47 UTC
f4762d9 Thomas B. Mooney 21 September 2016, 17:09:04 UTC Generate the FOF to pass to the tool. This test broke when the absolute path to the file changed. 21 September 2016, 17:09:04 UTC
569b086 APipe Tester 21 September 2016, 12:16:29 UTC Updated `gmt` tab completion. 21 September 2016, 12:16:29 UTC
804f9ab APipe Tester 21 September 2016, 12:15:48 UTC Updated `genome` tab completion. 21 September 2016, 12:15:48 UTC
23017e3 APipe Tester 21 September 2016, 12:14:23 UTC Updated class browser cache. 21 September 2016, 12:14:23 UTC
011bf32 Thomas B. Mooney 20 September 2016, 18:51:53 UTC Merge pull request #1570 from tmooney/remove_analysis_454 Remove `gmt analysis 454` tree. 20 September 2016, 18:51:53 UTC
5fda961 Thomas B. Mooney 20 September 2016, 18:51:36 UTC Merge pull request #1567 from tmooney/bed_to_vcf_converter_uses_correct_position Use position we calculated instead of printing start position from BED. 20 September 2016, 18:51:36 UTC
7512002 Jason Walker 20 September 2016, 18:19:05 UTC Merge pull request #1575 from susannasiebert/touch_file Create the temp_4type_output file if it doesn't exist after the R command is run 20 September 2016, 18:19:05 UTC
c2c0dd1 Susanna Kiwala 20 September 2016, 18:00:59 UTC Create the temp_4type_output file if it doesn't exist after the R command is run 20 September 2016, 18:00:59 UTC
c93cfe5 Feiyu Du 20 September 2016, 17:42:46 UTC Merge pull request #1574 from dufeiyu/update_blessed_builds Update blessed builds 20 September 2016, 17:42:46 UTC
1c8feda Feiyu Du 20 September 2016, 17:21:49 UTC update blessed builds 20 September 2016, 17:21:49 UTC
e9c47a5 Jason Walker 20 September 2016, 15:21:47 UTC Merge pull request #1573 from susannasiebert/touch_file Create the output file if it doesn't exist after the R command is run 20 September 2016, 15:21:47 UTC
8729cad Feiyu Du 19 September 2016, 21:45:43 UTC Merge pull request #1572 from dufeiyu/pindelRegion Add FT format field to pindelRegion vcf 19 September 2016, 21:45:43 UTC
a05cd8f Susanna Kiwala 19 September 2016, 21:15:41 UTC Create the output file if it doesn't exist after the R command is run 19 September 2016, 21:15:41 UTC
a93095b Thomas B. Mooney 19 September 2016, 19:26:27 UTC Merge pull request #1562 from tmooney/dont_bother_self_intersecting_cnmops Don't bother intersecting this file with itself. Return the one copy. 19 September 2016, 19:26:27 UTC
3f94356 Feiyu Du 19 September 2016, 15:09:14 UTC use File::Spec->join 19 September 2016, 15:09:14 UTC
92512d0 Feiyu Du 16 September 2016, 17:11:40 UTC Update homo_polymer list with min_length 7 16 September 2016, 17:11:40 UTC
7fb0f90 Feiyu Du 16 September 2016, 02:40:45 UTC Add FT format field to pindelRegion vcf 16 September 2016, 02:40:45 UTC
ac71c46 Thomas B. Mooney 15 September 2016, 21:18:50 UTC Use object properties instead of global variables to store positions. This isn't likely to matter too much--in practice this runs once and isn't multi-threaded or re-entrant--but it doesn't hurt anything! 15 September 2016, 21:18:50 UTC
857332c Thomas B. Mooney 15 September 2016, 20:36:50 UTC Remove `gmt analysis 454` tree. 15 September 2016, 20:36:50 UTC
5816b7f Thomas B. Mooney 15 September 2016, 20:35:05 UTC Remove `gmt capture mutations-from-group`. 15 September 2016, 20:35:05 UTC
de5babe Thomas B. Mooney 15 September 2016, 20:04:01 UTC Remove old CopyNumber ReadDepth tools. 15 September 2016, 20:04:01 UTC
2f00120 Thomas B. Mooney 15 September 2016, 19:44:49 UTC Use position we calculated instead of printing start position from BED. 15 September 2016, 19:44:49 UTC
93bcf79 Thomas B. Mooney 15 September 2016, 19:21:58 UTC Merge pull request #1565 from tmooney/drop_workorder_estimate_id The estimate_id column has been dropped from the Work Order table. 15 September 2016, 19:21:58 UTC
df9996f Thomas B. Mooney 15 September 2016, 17:52:18 UTC Remove old Varscan Copy-Number tools. 15 September 2016, 17:52:18 UTC
835fbc2 Thomas B. Mooney 15 September 2016, 17:20:48 UTC The estimate_id column has been dropped from the Work Order table. 15 September 2016, 17:20:48 UTC
c939a1f Thomas B. Mooney 15 September 2016, 17:14:44 UTC Remove out-dated bash completion helper. It contains a hard-coded /gsc/ path, and one that doesn't even point to the correct file path within the repository assuming someone did set it up that way! 15 September 2016, 17:14:44 UTC
42b6d63 Thomas B. Mooney 15 September 2016, 16:50:38 UTC Remove Genome::Utility::SystemSnapshot. This was related to the old "Benchmark" model type. 15 September 2016, 16:50:38 UTC
8faffed Feiyu Du 15 September 2016, 16:40:44 UTC Merge pull request #1561 from dufeiyu/vcf Make normal/tumor sample field real 15 September 2016, 16:40:44 UTC
90b7fb6 Thomas B. Mooney 15 September 2016, 15:18:53 UTC Don't bother intersecting this file with itself. Return the one copy. `bedtools intersect` seems to not be stable with regard to self-intersection. It's adding duplicate rows to the resulting file, which causes trouble for our R script. 15 September 2016, 15:18:53 UTC
12d6934 APipe Tester 14 September 2016, 12:17:57 UTC Updated `genome` tab completion. 14 September 2016, 12:17:57 UTC
2aeea96 APipe Tester 14 September 2016, 12:16:33 UTC Updated class browser cache. 14 September 2016, 12:16:33 UTC
39579bb Feiyu Du 14 September 2016, 03:18:16 UTC update unit test 14 September 2016, 03:18:16 UTC
de87ea6 Feiyu Du 13 September 2016, 18:10:46 UTC Make normal/tumor sample field real 13 September 2016, 18:10:46 UTC
ebe161a Thomas B. Mooney 13 September 2016, 15:09:35 UTC Merge pull request #1534 from tmooney/unarchive_instrument_data Unarchive command for AnPs using a Site::TGI Extension for LIMS data. 13 September 2016, 15:09:35 UTC
9f6e9ce Thomas B. Mooney 12 September 2016, 19:53:49 UTC Use status message. 12 September 2016, 19:53:49 UTC
31022e5 Thomas B. Mooney 12 September 2016, 19:52:26 UTC Spacing is important. (Typo fix.) 12 September 2016, 19:52:41 UTC
3d7cc46 Thomas B. Mooney 12 September 2016, 19:51:39 UTC Use App->init() and check that we were passed values. 12 September 2016, 19:51:39 UTC
750a8a0 Thomas B. Mooney 12 September 2016, 18:51:20 UTC Move $dv declaration closer to use. 12 September 2016, 18:51:20 UTC
ffa09eb Thomas B. Mooney 12 September 2016, 18:48:32 UTC Use allocation accessor from ObjectWithAllocations role. 12 September 2016, 18:48:32 UTC
bd72aa9 Thomas B. Mooney 12 September 2016, 18:46:31 UTC Find the dirname from the unarchive path. 12 September 2016, 18:46:31 UTC
7a8331a Eddie Belter 12 September 2016, 18:27:35 UTC Merge pull request #1558 from ebelter/library-is-rna Quote extraction types when determining is_rna 12 September 2016, 18:27:35 UTC
b815265 Thomas B. Mooney 08 September 2016, 20:24:00 UTC Only try to print the workflow if we have a process. 08 September 2016, 21:05:31 UTC
544e254 Thomas B. Mooney 15 August 2016, 14:16:01 UTC Don't commit when succeeding "inline" workflows. The caller running the inline workflow can handle that. 08 September 2016, 21:05:31 UTC
78c5cf7 Thomas B. Mooney 11 August 2016, 22:56:44 UTC Remove support for workflow_builder_backend of "workflow". 08 September 2016, 21:05:30 UTC
cb06a2e Thomas B. Mooney 11 August 2016, 22:57:35 UTC Set default backend to "inline". (For the record, locally at MGI there is a system-level default of "ptero".) 08 September 2016, 21:05:30 UTC
5b60742 Thomas B. Mooney 11 August 2016, 22:55:14 UTC Remove views for displaying Workflows. 08 September 2016, 21:05:30 UTC
043a3e2 Thomas B. Mooney 11 August 2016, 22:54:18 UTC Remove Workflow path from search engine page. 08 September 2016, 21:05:30 UTC
67e7f08 Thomas B. Mooney 11 August 2016, 22:19:35 UTC Remove outdated comments. 08 September 2016, 21:05:29 UTC
8ebe527 Thomas B. Mooney 11 August 2016, 21:58:10 UTC Don't use Workflow. 08 September 2016, 21:05:29 UTC
4293c6f Thomas B. Mooney 11 August 2016, 21:52:14 UTC Remove references to workflow instances. (The colum on Genome::Model::Event must remain for now for database compatibility.) 08 September 2016, 21:05:29 UTC
b947079 Thomas B. Mooney 11 August 2016, 21:49:31 UTC Remove "server-dispatch" and "job-dispatch" parameters. All building of builds now goes through the Process--even for "inline" workflows. Use the "workflow_builder_backend" config value "inline" to run inline instead of these parameters. 08 September 2016, 21:05:29 UTC
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