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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
f9d755c Susanna Siebert 16 February 2015, 17:54:34 UTC reimplementation of is not necessary because G::FL::processed_bed_file is already memoized 16 February 2015, 17:54:34 UTC
f2ef25b Thomas Mooney 16 February 2015, 16:42:23 UTC Don't try to add users to deleted results. 16 February 2015, 16:42:23 UTC
35fc353 Susanna Siebert 16 February 2015, 15:21:47 UTC remove column splitting capabilities 16 February 2015, 15:21:47 UTC
0293654 apregier 13 February 2015, 21:30:28 UTC Create a shell process for vep commands If vep commands are run stand-alone, create a basic process to satisfy the new requestor user requirement. 13 February 2015, 21:33:54 UTC
60576fd apregier 12 February 2015, 21:29:50 UTC Make a run_inline method on Process 13 February 2015, 21:33:53 UTC
bd46220 Susanna Siebert 13 February 2015, 20:53:35 UTC handle case where bed_entry isn't defined 13 February 2015, 20:53:35 UTC
a657764 Eddie Belter 13 February 2015, 20:41:35 UTC Merge pull request #474 from ebelter/bwamem-aligner-index-add-users BWAMEM AR: pass ref index users along to aligner index software result 13 February 2015, 20:41:35 UTC
3b1f33a Susanna Siebert 13 February 2015, 17:18:42 UTC only check the first 10 lines of the feature list 13 February 2015, 17:18:42 UTC
35c330a APipe Tester 13 February 2015, 13:16:16 UTC Updated `genome` tab completion. 13 February 2015, 13:16:16 UTC
98a653e APipe Tester 13 February 2015, 13:14:32 UTC Updated class browser cache. 13 February 2015, 13:14:32 UTC
5d0ad8a Eddie Belter 12 February 2015, 22:22:00 UTC BWAMEM AR: use _user_data_for_nested_results convenience method to pass users along 12 February 2015, 22:22:00 UTC
d62103a Thomas B. Mooney 12 February 2015, 22:12:33 UTC Merge pull request #468 from tmooney/dont_make_duplicate_users Defer SR user creation to commit time and lock to prevent duplicates. 12 February 2015, 22:12:33 UTC
346f8fa Eddie Belter 12 February 2015, 22:02:16 UTC BWAMEM AR: pass ref index users along to aligner index software result 12 February 2015, 22:02:16 UTC
d171cb9 Nathaniel Nutter 12 February 2015, 20:53:20 UTC Merge pull request #469 from nnutter/lock need to install handlers before backends start locking 12 February 2015, 20:53:20 UTC
6675de2 Ian Ferguson 12 February 2015, 20:10:34 UTC Merge pull request #473 from iferguson90/coverage-report-fix Fix duplicate models on coverage report summary 12 February 2015, 20:10:34 UTC
d7f20ee Ian Ferguson 12 February 2015, 19:54:06 UTC Fix duplicate models on coverage report summary 12 February 2015, 19:55:41 UTC
5f4e9cb Charles Lu 12 February 2015, 19:47:35 UTC Merge branch 'master' of https://github.com/genome/genome 12 February 2015, 19:47:35 UTC
93b463c Thomas Mooney 12 February 2015, 19:38:09 UTC Remove old test that uses live data. 12 February 2015, 19:38:09 UTC
f9d9a2d Thomas Mooney 12 February 2015, 18:57:33 UTC A test of the instrument-data alignment-bams command. 12 February 2015, 18:57:33 UTC
73c6723 Nathaniel Nutter 12 February 2015, 18:02:48 UTC Merge pull request #470 from nnutter/test-db fix option spec 12 February 2015, 18:02:48 UTC
d9d0b41 Susanna Siebert 12 February 2015, 17:25:15 UTC fail early if feature list contains invalid characters 12 February 2015, 17:52:18 UTC
6ee74f7 Thomas Mooney 12 February 2015, 17:09:24 UTC Rename variable: lane_bamqcpath -> lane_bamqc_path 12 February 2015, 17:09:24 UTC
5ba4fa9 Thomas Mooney 12 February 2015, 17:09:01 UTC Remove unneeded variables. 12 February 2015, 17:09:01 UTC
c463f15 Thomas Mooney 12 February 2015, 17:07:47 UTC "lane" is not a unique identifier. Use ID instead. 12 February 2015, 17:07:47 UTC
3d3603d Thomas Mooney 12 February 2015, 17:01:51 UTC Use a normal return value instead of passing in a reference. 12 February 2015, 17:04:22 UTC
7d3c63e Thomas Mooney 12 February 2015, 16:47:34 UTC Pass build to narrow down QC results. 12 February 2015, 17:03:48 UTC
e05a25c Thomas Mooney 12 February 2015, 16:39:56 UTC Use separated-value-writer. 12 February 2015, 17:03:48 UTC
8126c67 Thomas Mooney 12 February 2015, 16:24:55 UTC Specify build directly. 12 February 2015, 17:03:40 UTC
17c78ee Thomas Mooney 12 February 2015, 16:23:18 UTC Consolidate "InstrumentDataAlignmentBams" commands. 12 February 2015, 16:27:51 UTC
a820502 Avinash Ramu 12 February 2015, 15:47:46 UTC Merge pull request #453 from gatoravi/clinseq_dgidb_converge Migrate clinseq converge dgidb 12 February 2015, 15:47:46 UTC
857fab5 Thomas Mooney 12 February 2015, 14:07:11 UTC Remove useless constructor. 12 February 2015, 14:07:11 UTC
7dc0711 Nathaniel Nutter 12 February 2015, 07:59:47 UTC fix option spec I let the option spec get out of sync again. This fixes it for changes that were previously made to the case statement: - add the -m option - remove the -v option 12 February 2015, 08:00:47 UTC
90a418d Nathaniel Nutter 09 February 2015, 22:09:01 UTC need to install handlers before backends start locking 11 February 2015, 23:41:00 UTC
7e3f264 Thomas Mooney 11 February 2015, 23:31:51 UTC Add subtest to check that lock was released. 11 February 2015, 23:31:51 UTC
7189fb9 Thomas Mooney 11 February 2015, 23:22:40 UTC Add commits in tests with inline workflows before querying for users. 11 February 2015, 23:22:40 UTC
d82e09d Nathaniel Nutter 11 February 2015, 23:18:35 UTC Merge pull request #467 from nnutter/test-db more genome-env-next fixes/cleanup 11 February 2015, 23:18:35 UTC
0276d51 Nathaniel Nutter 11 February 2015, 21:46:21 UTC only run when these blocks without -D (DISABLE_DB) 11 February 2015, 21:46:21 UTC
3300ca4 Thomas Mooney 11 February 2015, 21:45:32 UTC Defer SR user creation to commit time and lock to prevent duplicates. 11 February 2015, 21:45:32 UTC
8dc2304 Nathaniel Nutter 10 February 2015, 23:54:11 UTC localize more variables 11 February 2015, 21:42:44 UTC
39d972e Nathaniel Nutter 10 February 2015, 23:53:31 UTC remove unused verbose option 11 February 2015, 21:42:43 UTC
bc24ff0 Nathaniel Nutter 11 February 2015, 21:24:56 UTC Merge pull request #462 from nnutter/test-db genome-env-next iteration 11 February 2015, 21:24:56 UTC
7a9fa8a Avinash Ramu 11 February 2015, 18:42:03 UTC remove \t and \n from beginning of messages. 11 February 2015, 18:42:37 UTC
78ea597 Avinash Ramu 11 February 2015, 18:32:36 UTC use separated value writer 11 February 2015, 18:32:36 UTC
e2412f7 Thomas B. Mooney 11 February 2015, 15:32:57 UTC Merge pull request #465 from tmooney/only_check_refseq_converter_existence Only check that converter exists during ROI validation. 11 February 2015, 15:32:57 UTC
c2b336b Susanna Siebert 11 February 2015, 14:38:41 UTC Merge pull request #464 from susannasiebert/variant_reporting_vaf_refactor Make vaf interpreters transient optional parameters 11 February 2015, 14:38:41 UTC
0fdaf8d Susanna Siebert 11 February 2015, 14:31:52 UTC Merge pull request #466 from susannasiebert/variant_reporting_libraries Change how the PerLibraryvafInterpreter handles planned libraries 11 February 2015, 14:31:52 UTC
258549f Thomas Mooney 10 February 2015, 14:31:31 UTC A few basic validation tests. 11 February 2015, 14:10:18 UTC
486e8f3 Susanna Siebert 11 February 2015, 14:06:50 UTC check that vaf interpreter has been created 11 February 2015, 14:06:50 UTC
4e9654a Eddie Belter 10 February 2015, 23:25:27 UTC Merge pull request #424 from ebelter/sra-2-bam InstData Import: update sra to bam for the fixed version of sam-dump. YAY! 10 February 2015, 23:25:27 UTC
eec88ac Feiyu Du 10 February 2015, 18:44:16 UTC update som-var long build 10 February 2015, 18:44:16 UTC
b12ea66 Charles Lu 10 February 2015, 16:44:34 UTC Merge branch 'master' of https://github.com/genome/genome 10 February 2015, 16:44:34 UTC
103e382 Susanna Siebert 10 February 2015, 15:19:53 UTC additional libraries get vaf field populated with interpretation_null_character 10 February 2015, 15:19:53 UTC
7fac81c Thomas Mooney 10 February 2015, 14:31:04 UTC _faster_get was changed to always return a scalar. 10 February 2015, 14:31:04 UTC
a80ee80 Thomas Mooney 10 February 2015, 13:56:16 UTC Only check for converter's existence during ROI validation. 10 February 2015, 13:56:16 UTC
7ed773c Susanna Siebert 09 February 2015, 22:39:57 UTC restrict the interpretations fields to the planned libraries 09 February 2015, 22:39:57 UTC
79c4dbd Avinash Ramu 09 February 2015, 22:26:06 UTC rename method 09 February 2015, 22:26:06 UTC
7fe84d9 Avinash Ramu 09 February 2015, 22:25:07 UTC check for subject_name 09 February 2015, 22:25:07 UTC
e6e508d Avinash Ramu 09 February 2015, 22:03:07 UTC Remove unwanted newlines in messages. 09 February 2015, 22:03:07 UTC
7ca2538 Nathaniel Nutter 09 February 2015, 21:05:21 UTC give the sqitch repo the same options as ur/workflow 09 February 2015, 21:05:21 UTC
56b361f Susanna Siebert 09 February 2015, 20:37:04 UTC make vaf interpreters transient optional parameters 09 February 2015, 21:03:32 UTC
80258fc Nathaniel Nutter 09 February 2015, 20:30:09 UTC show "nothing to deploy" status when no migrations 09 February 2015, 20:31:10 UTC
e08df3e Nathaniel Nutter 09 February 2015, 20:20:14 UTC use new sqitch/genome submodule 09 February 2015, 20:31:09 UTC
b2e4a82 Nathaniel Nutter 09 February 2015, 20:03:48 UTC setup_test_db should be a no-op if DB is disabled 09 February 2015, 20:31:09 UTC
f65c0a7 Nathaniel Nutter 09 February 2015, 19:53:14 UTC pull prepare_submodules out of set_defaults prepare_submodules seems like a weird side-effect for set_defaults so pull it out. Since set_defaults determines whether some submodules are required track that state separately using append_submodule. 09 February 2015, 20:31:08 UTC
511c1bf Nathaniel Nutter 09 February 2015, 19:46:07 UTC disabling DB implies disabling DB migrations 09 February 2015, 20:31:07 UTC
d255765 Nathaniel Nutter 09 February 2015, 19:44:48 UTC missed reference to the old -S/-s options 09 February 2015, 20:31:06 UTC
02cf1a5 Nathaniel Nutter 09 February 2015, 16:43:01 UTC add template to temp dir 09 February 2015, 20:31:06 UTC
4d61a23 Nathaniel Nutter 09 February 2015, 20:30:50 UTC Merge pull request #461 from nnutter/sqitch move sqitch/gms to submodule sqitch/genome 09 February 2015, 20:30:50 UTC
7dbc814 Nathaniel Nutter 09 February 2015, 19:19:33 UTC move sqitch/gms to submodule sqitch/genome This was moved to a different directory so as not to cause errors when switching between commits before and after this. 09 February 2015, 20:21:19 UTC
3f9792e Nathaniel Nutter 09 February 2015, 19:15:31 UTC Merge pull request #458 from nnutter/master add scope argument to POD 09 February 2015, 19:15:31 UTC
f457155 APipe Tester 09 February 2015, 15:30:42 UTC updated jenkins submodule to 558eb8b 09 February 2015, 16:46:24 UTC
627d945 APipe Tester 09 February 2015, 15:30:28 UTC updated ur submodule to 4961c70 09 February 2015, 16:46:24 UTC
43f1b8c Susanna Siebert 09 February 2015, 15:58:22 UTC Merge pull request #450 from susannasiebert/variant_reporting_vaf_refactor CHANGELOG: This is a refactor of the vaf and many-sample-vaf interpreters in the variant reporting subsystem. Changes to your plan files are necessary if they use either of these interpreter. Please consult https://confluence.gsc.wustl.edu/display/BIO/Vaf+Interpreters+Refactor+Feb+2015 for instructions. 09 February 2015, 15:58:22 UTC
e76f67e Nathaniel Nutter 09 February 2015, 15:27:52 UTC Merge pull request #460 from nnutter/test-db update genome-env-next default DB snapshot 09 February 2015, 15:27:52 UTC
e650ee5 Nathaniel Nutter 09 February 2015, 15:26:35 UTC fix typo 09 February 2015, 15:26:35 UTC
08c372b Nathaniel Nutter 09 February 2015, 15:18:03 UTC update genome-env-next default DB snapshot 09 February 2015, 15:18:50 UTC
2070701 Thomas B. Mooney 09 February 2015, 15:07:21 UTC Merge pull request #448 from tmooney/dont_unarchive_purged_allocations Trust an Allocation's Status When Deciding if Archived 09 February 2015, 15:07:21 UTC
943d82c Anthony Brummett 08 February 2015, 17:27:27 UTC Merge pull request #455 from brummett/redirect-redux Another try at fixing STDOUT and STDERR redirection 08 February 2015, 17:27:27 UTC
40774a0 Anthony Brummett 07 February 2015, 16:01:47 UTC Merge branch 'master' into redirect-redux-merge 07 February 2015, 16:01:47 UTC
77c3c2a Nathaniel Nutter 06 February 2015, 23:25:52 UTC Merge pull request #459 from nnutter/bam-window new expected output due to bam-window update 06 February 2015, 23:25:52 UTC
0a60c27 Nathaniel Nutter 06 February 2015, 23:17:12 UTC Merge pull request #441 from nnutter/new-env genome-env rewrite/refactor 06 February 2015, 23:17:12 UTC
4ac5110 Nathaniel Nutter 06 February 2015, 23:03:31 UTC new expected output due to bam-window update 06 February 2015, 23:03:31 UTC
f454984 Nathaniel Nutter 06 February 2015, 22:41:13 UTC missed getopts spec when renaming 06 February 2015, 22:41:13 UTC
a7f68c1 Nathaniel Nutter 06 February 2015, 21:08:26 UTC add scope argument to POD 06 February 2015, 21:10:11 UTC
ba45199 Chris Miller 06 February 2015, 20:54:35 UTC Merge pull request #457 from chrisamiller/master fixing typo that caused long indel rcnts to be blank in edge cases 06 February 2015, 20:54:35 UTC
ba55779 Anthony Brummett 06 February 2015, 20:36:03 UTC preserve old behavior of always adding an extra newline to STDOUT Reverted the test to look for this newline again 06 February 2015, 20:36:03 UTC
b644c0b Chris Miller 06 February 2015, 18:00:24 UTC fixing typo that caused long indel rcnts to be blank in edge cases 06 February 2015, 18:00:37 UTC
7c2b360 Susanna Siebert 06 February 2015, 16:03:54 UTC have available_libraries subroutine return the Set::Scalar 06 February 2015, 16:03:54 UTC
618f86e Anthony Brummett 06 February 2015, 15:47:12 UTC Merge pull request #452 from brummett/relay-errors Relay child process' STDERR as error_message()s 06 February 2015, 15:47:12 UTC
1bc0db0 Anthony Brummett 06 February 2015, 15:44:30 UTC Merge pull request #454 from brummett/newline missing newline is messing up TAP output 06 February 2015, 15:44:30 UTC
fa31368 Susanna Siebert 06 February 2015, 15:32:17 UTC get rid of vaf_results subroutines 06 February 2015, 15:32:17 UTC
74edb34 Anthony Brummett 06 February 2015, 15:31:21 UTC Fix the Sys-shellcmd.t 'redirected child stdout to a file' test. The extra newline is now only printed if STDOUT was _not_ redirected. This change means the output file now contains the real output of the child program. Previous code waited until the child process was done, then printed a newline to STDOUT while it was still possibly redirected. 06 February 2015, 15:31:21 UTC
d1b114d Anthony Brummett 06 February 2015, 15:27:11 UTC Fix the Sys-shellcmd.t 'Run echo with stdout redirected' test We only need to print a newline if STDOUT was _not_ redirected. This is to compensate in case the child process didn't print a newline after it's last print, which would screw up TAP in the parent process (which prints to STDOUT). If STDOUT is redirected, then whatever the child process prints there won't have any effect on the parent process' TAP output. Previous shellcmd() code waited until the child program was done, then printed a newline to STDOUT while it was still possibly redirected. 06 February 2015, 15:27:11 UTC
55f2e42 Susanna Siebert 06 February 2015, 15:27:10 UTC remove unused use statements 06 February 2015, 15:27:10 UTC
024ea89 APipe Tester 06 February 2015, 13:16:29 UTC Updated `gmt` tab completion. 06 February 2015, 13:16:29 UTC
9a6172c APipe Tester 06 February 2015, 13:15:48 UTC Updated `genome` tab completion. 06 February 2015, 13:15:48 UTC
4412a65 APipe Tester 06 February 2015, 13:14:17 UTC Updated class browser cache. 06 February 2015, 13:14:17 UTC
1ec4f39 Nathaniel Nutter 05 February 2015, 21:28:40 UTC add comments for functions 06 February 2015, 00:19:43 UTC
4432b23 Nathaniel Nutter 05 February 2015, 21:28:22 UTC relocate function 06 February 2015, 00:19:43 UTC
ce7410d Nathaniel Nutter 05 February 2015, 20:58:38 UTC remove unused "gms-config" variable 06 February 2015, 00:19:42 UTC
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