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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
caef1d8 Thomas B. Mooney 23 February 2015, 21:01:52 UTC Merge pull request #497 from tmooney/set_gtmp_in_varscan_validation Reserve tmp since our output is written there before being allocated. 23 February 2015, 21:01:52 UTC
f773fcf Nathaniel Nutter 22 February 2015, 19:24:14 UTC Merge pull request #499 from nnutter/test-db update default DB snapshot 22 February 2015, 19:24:14 UTC
950486b Nathaniel Nutter 22 February 2015, 18:30:51 UTC add basic tests for the -m/-M options 22 February 2015, 18:30:51 UTC
3efe766 APipe Tester 22 February 2015, 16:33:35 UTC updated ur submodule to 7f8f8d4 22 February 2015, 16:33:35 UTC
7674520 Nathaniel Nutter 22 February 2015, 16:27:13 UTC update default DB snapshot Update the default DB snapshot to a snapshot that should be able to run the model tests. 22 February 2015, 16:27:13 UTC
23a5ccf APipe Tester 20 February 2015, 13:16:58 UTC Updated `gmt` tab completion. 20 February 2015, 13:16:58 UTC
e66dde4 APipe Tester 20 February 2015, 13:16:14 UTC Updated `genome` tab completion. 20 February 2015, 13:16:14 UTC
3aaf22b Eddie Belter 19 February 2015, 23:03:27 UTC Merge pull request #493 from ebelter/sample-import-5 Sample Import 19 February 2015, 23:03:27 UTC
6c4355f Thomas Mooney 19 February 2015, 22:30:50 UTC Reserve tmp since our output is written there before being allocated. 19 February 2015, 22:30:50 UTC
c6490d7 Nathaniel Nutter 19 February 2015, 21:11:35 UTC Merge pull request #389 from clu76/master added option to change indel size and define reference transcript version 19 February 2015, 21:11:35 UTC
1a7fcb6 Charles Lu 19 February 2015, 20:47:13 UTC added $self to function "process_somatic_variation_models" 19 February 2015, 20:47:13 UTC
1d935e2 Charles Lu 19 February 2015, 20:43:30 UTC All stderr message changed to *_message function 19 February 2015, 20:43:30 UTC
904d6ff Nathaniel Nutter 19 February 2015, 20:22:36 UTC Merge pull request #494 from nnutter/test-db add some test coverage for `genome-env-next` 19 February 2015, 20:22:36 UTC
a465294 Nathaniel Nutter 19 February 2015, 18:24:34 UTC extract method: assert_module_found 19 February 2015, 18:24:34 UTC
ed1e13e Nathaniel Nutter 19 February 2015, 18:21:47 UTC extract method: assert_module_missing 19 February 2015, 18:24:20 UTC
44e5f82 Susanna Siebert 19 February 2015, 18:09:37 UTC Merge pull request #486 from susannasiebert/variant_reporting_merge_reports Limit MergeReports to only two files 19 February 2015, 18:09:37 UTC
7c3b074 Nathaniel Nutter 19 February 2015, 18:05:03 UTC remove another debug statement 19 February 2015, 18:05:03 UTC
7499c0d Nathaniel Nutter 19 February 2015, 18:02:41 UTC remove debug statement 19 February 2015, 18:02:41 UTC
c9bc963 Nathaniel Nutter 19 February 2015, 18:00:22 UTC Merge pull request #496 from nnutter/db-snapshot update default DB snapshot 19 February 2015, 18:00:22 UTC
997decc Susanna Siebert 19 February 2015, 17:28:23 UTC has_size needs to be transient optional 19 February 2015, 17:28:23 UTC
8e61b6c Susanna Siebert 19 February 2015, 16:57:53 UTC return undef for has_size if report_path hasn't been set 19 February 2015, 16:57:53 UTC
b312f04 Susanna Siebert 19 February 2015, 16:57:17 UTC return undef for report_path if output_dir isn't set yet 19 February 2015, 16:57:17 UTC
2678344 Thomas B. Mooney 19 February 2015, 15:47:15 UTC Merge pull request #487 from tmooney/taxon_view_test_factory Use a Test Factory Taxon in View Tests 19 February 2015, 15:47:15 UTC
6d979af Thomas B. Mooney 19 February 2015, 14:12:40 UTC Merge pull request #492 from tmooney/also_ensure_sr_exists Don't try to add users to deleted results. 19 February 2015, 14:12:40 UTC
d5e48c5 Susanna Siebert 19 February 2015, 13:52:24 UTC make has_size a transient attribute 19 February 2015, 13:52:24 UTC
1a467c0 APipe Tester 19 February 2015, 13:16:40 UTC Updated `genome` tab completion. 19 February 2015, 13:16:40 UTC
da6f079 APipe Tester 19 February 2015, 13:14:58 UTC Updated class browser cache. 19 February 2015, 13:14:58 UTC
98f5720 Nathaniel Nutter 19 February 2015, 07:14:36 UTC update default DB snapshot 19 February 2015, 07:14:36 UTC
182b971 Nathaniel Nutter 19 February 2015, 01:04:17 UTC document lack of test coverage 19 February 2015, 01:05:44 UTC
aacb772 Nathaniel Nutter 19 February 2015, 01:02:15 UTC add submodule.bats 19 February 2015, 01:05:43 UTC
a7523d2 Nathaniel Nutter 19 February 2015, 00:53:15 UTC add some basic acceptance tests for `genome-env-next` 19 February 2015, 01:05:40 UTC
0934256 Nathaniel Nutter 18 February 2015, 23:08:38 UTC fix unexpected behaviors when using the -U or -W options 19 February 2015, 01:05:39 UTC
34517d7 Nathaniel Nutter 13 February 2015, 20:07:35 UTC restore set options 19 February 2015, 01:05:38 UTC
d167abc Eddie Belter 19 February 2015, 00:03:17 UTC Sample Import: rename _import to _get_or_create_individual 19 February 2015, 00:03:17 UTC
e73c189 Eddie Belter 18 February 2015, 23:55:16 UTC Sample Import: remove _get_or_create_library 18 February 2015, 23:55:16 UTC
c8b5d96 Eddie Belter 18 February 2015, 23:53:41 UTC Sample Import: move _create_sample into main execute method 18 February 2015, 23:53:41 UTC
53a549f Eddie Belter 18 February 2015, 23:44:03 UTC Merge pull request #490 from ebelter/sample-import-4 Sample Import: add taxon as an optional command param 18 February 2015, 23:44:03 UTC
22d0052 Eddie Belter 18 February 2015, 23:26:12 UTC Merge remote-tracking branch 'origin' into sample-import-4 Conflicts: lib/perl/Genome/Sample/Command/Import/Base.t 18 February 2015, 23:26:12 UTC
d490702 Eddie Belter 18 February 2015, 23:14:59 UTC Merge pull request #489 from ebelter/sample-import-3 Sample Import: Library Handling Update 18 February 2015, 23:14:59 UTC
d4f655c Thomas Mooney 18 February 2015, 21:42:01 UTC Use grep for clarity. 18 February 2015, 21:42:01 UTC
ea73109 Thomas Mooney 18 February 2015, 21:27:38 UTC Also don't try to add users to deleted objects. 18 February 2015, 21:27:38 UTC
84215b5 Eddie Belter 18 February 2015, 21:14:39 UTC Sample Import: transpose the e and h in teh per Tom's request 18 February 2015, 21:14:39 UTC
8d2f9d3 Eddie Belter 18 February 2015, 21:01:56 UTC Sample Import: remove unsused taxon from test. 18 February 2015, 21:01:56 UTC
e021c01 Susanna Siebert 18 February 2015, 17:46:00 UTC remove unnecessary call to class 18 February 2015, 17:46:00 UTC
5b7fc43 Thomas B. Mooney 18 February 2015, 16:46:42 UTC Merge pull request #483 from tmooney/run_reports_only_requires_bam Relax requirements for scheduling reference alignment reports. 18 February 2015, 16:46:42 UTC
25fcd60 Thomas B. Mooney 18 February 2015, 16:46:25 UTC Merge pull request #472 from tmooney/deduplicate_and_improve_idab_commands Deduplicate InstrumentData AlignmentBams commands 18 February 2015, 16:46:25 UTC
372d719 Susanna Siebert 18 February 2015, 15:38:05 UTC handle determination of base_report and supplemental_report for merging more gracefully 18 February 2015, 15:38:05 UTC
d28c2c9 Susanna Siebert 18 February 2015, 15:32:11 UTC don't instantiate result_class to get merge parameters 18 February 2015, 15:32:11 UTC
220ac77 Susanna Siebert 18 February 2015, 15:29:45 UTC remove unneeded get_reports_with_size subroutine 18 February 2015, 15:29:45 UTC
1c827e0 Susanna Siebert 18 February 2015, 15:29:19 UTC small refactor of merge_files to get rid of @reports_with_size 18 February 2015, 15:29:19 UTC
cf09a3d Susanna Siebert 18 February 2015, 15:22:20 UTC make handling of two empty files more readable 18 February 2015, 15:22:20 UTC
6bc3271 Susanna Siebert 18 February 2015, 15:19:55 UTC clean up validation 18 February 2015, 15:19:55 UTC
c2829d8 Susanna Siebert 18 February 2015, 15:16:37 UTC implement a has_size subroutine on MergeCompatible 18 February 2015, 15:16:37 UTC
c58f73f Allison Penner Regier 18 February 2015, 14:51:25 UTC Merge pull request #484 from apregier/make_vep_wrapper_more_robust Make vep wrapper more robust 18 February 2015, 14:51:25 UTC
a113123 APipe Tester 18 February 2015, 13:16:03 UTC Updated `genome` tab completion. 18 February 2015, 13:16:03 UTC
6e8046c APipe Tester 18 February 2015, 13:14:22 UTC Updated class browser cache. 18 February 2015, 13:14:22 UTC
ac195bf Thomas B. Mooney 18 February 2015, 00:00:38 UTC Merge pull request #482 from tmooney/respect_config_in_assign_all Respect Config when assigning all "Compatible Instrument Data" 18 February 2015, 00:00:38 UTC
74b8295 Thomas Mooney 17 February 2015, 23:11:59 UTC Add new test for AnalysisProject case in all-compatible. 17 February 2015, 23:11:59 UTC
a8e0153 Eddie Belter 17 February 2015, 23:09:08 UTC Sample Import: add taxon as an optional command param 17 February 2015, 23:09:08 UTC
492e843 Travis Abbott 17 February 2015, 22:32:15 UTC Merge pull request #488 from tabbott/jx-vcfreport-version update gmt joinx vcf-report to check versions properly 17 February 2015, 22:32:15 UTC
0140deb Eddie Belter 17 February 2015, 21:37:10 UTC Sample Import: move library get/create into main execute method 17 February 2015, 22:13:12 UTC
7816d6d Travis Abbott 17 February 2015, 21:46:51 UTC update gmt joinx vcf-report to check versions properly it was using floating point comparisons the 'minimum version' check. the base class already had a "check_minimum_version" method that does the right thing. added a test too. 17 February 2015, 21:57:25 UTC
8363d4b Thomas Mooney 17 February 2015, 21:47:25 UTC Stop pretending we're going to do diffs. 17 February 2015, 21:47:25 UTC
db8a797 Thomas Mooney 17 February 2015, 21:45:43 UTC Use test taxon. Existing mouse taxon has lots of data and makes this test run excessively long. 17 February 2015, 21:45:43 UTC
8b2cc5c Thomas Mooney 17 February 2015, 21:45:06 UTC Ensure NO_COMMIT is set. 17 February 2015, 21:45:06 UTC
665c768 Eddie Belter 17 February 2015, 21:34:58 UTC Sample Import: update tests 17 February 2015, 21:34:58 UTC
53c3314 Eddie Belter 17 February 2015, 21:30:10 UTC Sample Import: check if library is created already 17 February 2015, 21:30:10 UTC
6e119e4 Eddie Belter 17 February 2015, 21:24:49 UTC Sample Import: move set_library_params into _create_library 17 February 2015, 21:24:49 UTC
73bdfc0 Eddie Belter 17 February 2015, 21:22:24 UTC Sample Import: move library name to class def 17 February 2015, 21:22:24 UTC
e8267e3 apregier 17 February 2015, 21:21:49 UTC Use test name for reference items 17 February 2015, 21:21:49 UTC
ee487fa Eddie Belter 17 February 2015, 21:18:37 UTC Sample Import: make library extension a command property and stop pasing it around as a param 17 February 2015, 21:19:30 UTC
9f99665 Eddie Belter 17 February 2015, 21:13:04 UTC Merge pull request #485 from ebelter/sample-import-2 Sample Importer Attribute Cleanup 17 February 2015, 21:13:04 UTC
b4f7e6c Susanna Siebert 17 February 2015, 20:38:45 UTC remove use_header_from and use the base_report's header instead 17 February 2015, 20:38:45 UTC
f2f428f Eddie Belter 17 February 2015, 20:04:43 UTC Sample Importer: use HASH instead of Hash in attribute property defs 17 February 2015, 20:04:43 UTC
2e44892 Eddie Belter 17 February 2015, 19:37:02 UTC Sample Import: use library attr accessory when setting library attributes 17 February 2015, 19:37:02 UTC
1a975df Eddie Belter 17 February 2015, 19:18:24 UTC Sample Import: combine incoming attribute resolution into one method 17 February 2015, 19:21:46 UTC
c7fb8d5 Susanna Siebert 17 February 2015, 19:15:10 UTC use base_report instead of first report_results 17 February 2015, 19:15:10 UTC
1f4b106 Eddie Belter 17 February 2015, 19:13:10 UTC Sample Import: stop updating attributes on existing sample 17 February 2015, 19:13:23 UTC
c78c4f7 Eddie Belter 17 February 2015, 19:11:04 UTC Sample Import: stop passing taxon name around 17 February 2015, 19:11:04 UTC
53d9099 Eddie Belter 17 February 2015, 19:08:13 UTC Sample Import: mostly stop passing library attributes around 17 February 2015, 19:08:13 UTC
b7dd6d1 Susanna Siebert 17 February 2015, 19:07:54 UTC Split up report_results into a base_report and a supplemental_report This will ensure that we only ever supply two reports to be merged and that one of them (the base_report) will be handled as the primary one 17 February 2015, 19:07:54 UTC
c202f7e Eddie Belter 17 February 2015, 19:06:00 UTC Sample Import: stop passing sample attributes around 17 February 2015, 19:06:00 UTC
4af755d Eddie Belter 17 February 2015, 18:48:33 UTC Sample Import: stop passing individual attributes around 17 February 2015, 18:48:33 UTC
4cfca52 apregier 17 February 2015, 17:10:54 UTC Don't swallow error message with the eval 17 February 2015, 18:33:43 UTC
a52adcc apregier 11 February 2015, 18:40:16 UTC Don't rely on test name for annotation reference objects 17 February 2015, 18:33:42 UTC
d0d48a8 Eddie Belter 17 February 2015, 18:18:48 UTC Merge pull request #481 from ebelter/sample-import-1 Sample Import: remove _created_objects method 17 February 2015, 18:18:48 UTC
5334c80 Allison Penner Regier 17 February 2015, 17:16:03 UTC Merge pull request #476 from apregier/vep_standalone_process Vep standalone process 17 February 2015, 17:16:03 UTC
4e70ee8 Thomas Mooney 17 February 2015, 17:07:14 UTC Update blessed build to account for different QC paths and results 17 February 2015, 17:07:14 UTC
93ffc47 Thomas Mooney 17 February 2015, 16:34:28 UTC Relax requirements for scheduling reference alignment reports. 17 February 2015, 16:34:28 UTC
2a9d368 Susanna Siebert 17 February 2015, 14:57:08 UTC Merge pull request #478 from susannasiebert/variant_reporting_merge_reports Remove column splitting capabilities from MergedReport 17 February 2015, 14:57:08 UTC
2e1dc8e Thomas Mooney 16 February 2015, 22:16:13 UTC Now that "all-compatible" respects AnPs, remove separate assign command. 16 February 2015, 23:56:42 UTC
fdab5ab Thomas Mooney 16 February 2015, 22:14:59 UTC Only mock up the parser part configuration. 16 February 2015, 23:56:42 UTC
a257d2e Thomas Mooney 16 February 2015, 22:05:53 UTC Add newline at EOF 16 February 2015, 23:56:41 UTC
964c3cf Thomas Mooney 16 February 2015, 22:05:19 UTC Add a default run-as to test-factory analysis-projects. 16 February 2015, 23:56:41 UTC
3d0909e Thomas Mooney 16 February 2015, 19:12:22 UTC Respect configuration when deciding compatible instrument data. 16 February 2015, 23:56:41 UTC
ef3abda Thomas B. Mooney 16 February 2015, 22:47:02 UTC Merge pull request #479 from tmooney/dont_assign_users_to_deleted_objects Don't try to add users to deleted results. 16 February 2015, 22:47:02 UTC
c32ee12 Eddie Belter 16 February 2015, 20:09:39 UTC Sample Import: remove _created_objects method 16 February 2015, 20:09:39 UTC
00873f7 Thomas Mooney 16 February 2015, 18:40:54 UTC Don't create an unlock observer if we haven't got any locks. 16 February 2015, 18:40:54 UTC
6d04613 Susanna Siebert 16 February 2015, 18:28:09 UTC Merge pull request #471 from susannasiebert/variant_reporting_feature_list Variant reporting: fail vep annotation early if feature list contains invalid characters 16 February 2015, 18:28:09 UTC
788856d Susanna Siebert 16 February 2015, 17:55:01 UTC specify cache for process_bed_file memoization 16 February 2015, 17:55:01 UTC
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