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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
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
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
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
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
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
15d8c3b Nathaniel Nutter 05 February 2015, 20:52:18 UTC move local variables next to the function they are scoping 06 February 2015, 00:19:42 UTC
7de5105 Nathaniel Nutter 05 February 2015, 20:51:44 UTC allow external configuration of test-db 06 February 2015, 00:19:41 UTC
a636dd3 Nathaniel Nutter 05 February 2015, 20:46:07 UTC extract function to set default values 06 February 2015, 00:19:40 UTC
b686a13 Nathaniel Nutter 05 February 2015, 20:21:52 UTC deploy sqitch migrations without modifying repo 06 February 2015, 00:19:29 UTC
b09d768 Nathaniel Nutter 05 February 2015, 20:11:36 UTC rename DB snapshot related variables and options To avoid confusion with Genome snapshots be more specific that this is a DB snapshot. 06 February 2015, 00:19:27 UTC
e9308e0 Nathaniel Nutter 05 February 2015, 20:09:10 UTC validate shell earlier 06 February 2015, 00:19:27 UTC
c234081 Nathaniel Nutter 05 February 2015, 17:16:39 UTC rename variable for better consistency 06 February 2015, 00:19:26 UTC
038b9f2 Nathaniel Nutter 05 February 2015, 17:10:02 UTC fix bash paths 06 February 2015, 00:19:26 UTC
839a4a9 Nathaniel Nutter 05 February 2015, 17:07:59 UTC fix unbound variable error 06 February 2015, 00:19:25 UTC
a5ca928 Nathaniel Nutter 03 February 2015, 20:36:41 UTC review fatal codes 06 February 2015, 00:19:24 UTC
fe2e7f7 Nathaniel Nutter 03 February 2015, 20:33:26 UTC review fatal messages 06 February 2015, 00:19:23 UTC
2636543 Nathaniel Nutter 03 February 2015, 20:14:19 UTC test for existance of 'test-db' 06 February 2015, 00:19:23 UTC
468bb73 Nathaniel Nutter 03 February 2015, 20:09:10 UTC add 'fatal' function 06 February 2015, 00:19:22 UTC
b9db850 Nathaniel Nutter 03 February 2015, 19:58:52 UTC test for existance of 'grep' 06 February 2015, 00:19:21 UTC
e415a5a Nathaniel Nutter 03 February 2015, 19:56:11 UTC test for existance of 'sqlite3' 06 February 2015, 00:19:21 UTC
1981cf5 Nathaniel Nutter 03 February 2015, 19:54:01 UTC test for existance of 'sqitch' 06 February 2015, 00:19:20 UTC
abfa6d8 Nathaniel Nutter 03 February 2015, 19:51:54 UTC test for existance of 'git' 06 February 2015, 00:19:20 UTC
bd925b0 Nathaniel Nutter 03 February 2015, 19:50:18 UTC move block to bottom to allow use of local functions 06 February 2015, 00:19:19 UTC
2ec8280 Nathaniel Nutter 03 February 2015, 19:44:25 UTC homogenize coding style 06 February 2015, 00:19:18 UTC
7a34ea5 Nathaniel Nutter 03 February 2015, 19:33:46 UTC remove unused submodules 06 February 2015, 00:19:18 UTC
f620156 Nathaniel Nutter 03 February 2015, 19:21:21 UTC shorten error message 06 February 2015, 00:19:17 UTC
91ac755 Nathaniel Nutter 03 February 2015, 19:20:54 UTC enable errexit, pipefail, and nounset 06 February 2015, 00:19:16 UTC
278fa2b Nathaniel Nutter 03 February 2015, 19:08:09 UTC simplify SUBMODULES 06 February 2015, 00:19:16 UTC
b6089ce Nathaniel Nutter 03 February 2015, 19:07:45 UTC TOP is already defined 06 February 2015, 00:19:15 UTC
2e8949a Nathaniel Nutter 03 February 2015, 18:57:17 UTC remove delegating message 06 February 2015, 00:19:15 UTC
00f6691 Nathaniel Nutter 03 February 2015, 18:56:43 UTC avoid accidental infinite re-exec 06 February 2015, 00:19:14 UTC
f4c07c0 Nathaniel Nutter 03 February 2015, 18:46:00 UTC remove usage of 'wtf' 06 February 2015, 00:19:13 UTC
d7861db Nathaniel Nutter 03 February 2015, 18:36:08 UTC rename 'err' to 'log.error' 06 February 2015, 00:19:13 UTC
c28f5f9 Nathaniel Nutter 03 February 2015, 18:34:51 UTC rename 'stderr' to 'log.info' 06 February 2015, 00:19:12 UTC
41dc019 Nathaniel Nutter 03 February 2015, 18:30:28 UTC convert 'echo ... 1>&2' to 'stderr ...' 06 February 2015, 00:19:11 UTC
af05603 Nathaniel Nutter 14 January 2015, 22:08:25 UTC genome-env rewrite/refactor This pulls in code that was in the apipe-ci repo, adds more control to the constructed env through the use of options, and adds support for using a test database. 06 February 2015, 00:19:11 UTC
98c0aa2 Anthony Brummett 06 February 2015, 00:08:04 UTC Exit the process if exec fails Since this is inside of an eval{}, die() here wouldn't terminate the process. 06 February 2015, 00:08:04 UTC
d097239 Nathaniel Nutter 05 February 2015, 23:55:34 UTC Merge pull request #449 from nnutter/summary protect against corrupted Workflow::Models 05 February 2015, 23:55:34 UTC
d28f884 Anthony Brummett 05 February 2015, 23:54:36 UTC Another try at fixing STDOUT and STDERR redirection This supercedes e4ae511. The previous commit would have caused our web server to wig out. See the message in commit 0d56bbc for why. 05 February 2015, 23:54:36 UTC
2a270f7 Anthony Brummett 05 February 2015, 23:00:36 UTC missing newline is messing up TAP output 05 February 2015, 23:00:49 UTC
0579ea9 Thomas B. Mooney 05 February 2015, 22:23:48 UTC Merge pull request #444 from tmooney/even_more_reference_matching_for_fl_merge Add Common Reference Combination Cases in FeatureList Merge 05 February 2015, 22:23:48 UTC
e959370 Anthony Brummett 05 February 2015, 21:18:12 UTC Merge pull request #451 from brummett/fix-redirection Properly scope the saved STDOUT and STDERR handles 05 February 2015, 21:18:12 UTC
ed93d15 Anthony Brummett 05 February 2015, 20:26:09 UTC Relay child process' STDERR as error_message()s the old code wasn't doing what it thought it was doing 05 February 2015, 21:15:57 UTC
e4ae511 Anthony Brummett 05 February 2015, 20:00:01 UTC Properly scope the saved STDOUT and STDERR handles This should fix the two tests hanging on Jenkins: InstrumentData/Command/Import/Basic_sra.t InstrumentData/Command/Import/WorkFlow/SraToBam.t The problem is that Genome::InstrumentData::Command::Import::WorkFlow::SraToBam::do_shellcmd_with_stdout() is reading from a file of saved STDERR of a child process run with Genome::Sys::shellcmd() and printing it to its own STDERR. However, the current process' STDERR is also printing to that same file. The tests hang because do_shellcmd_with_stdout() never gets to the end of the file (it's filling it as it's reading). I'm not sure what the _actual_ bug is, but this seems to fix it, while removing global filehandle variables. 05 February 2015, 20:00:01 UTC
16cd42d Jim Weible 05 February 2015, 19:57:02 UTC Merge pull request #446 from jweible/AUE-388 AUE 388 05 February 2015, 19:57:02 UTC
c917112 apregier 05 February 2015, 16:51:24 UTC Merge pull request #447 from apregier/new_picard_option New picard option 05 February 2015, 16:51:24 UTC
cbee9d0 Jim Weible 05 February 2015, 16:22:46 UTC call Genome::Command::Viewer->get_terminal_width directly 05 February 2015, 16:22:46 UTC
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