swh:1:snp:5789d5563ae0ff1fac9d4620526a6e02863df326

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Revision Author Date Message Commit Date
5e45049 Merge pull request #1422 from susannasiebert/clinseq_summarizesvs ClinSeq SummarizeSvs uses test data for is test 16 May 2016, 17:12:59 UTC
64fa671 ClinSeq SummarizeSvs uses test data for is test 13 May 2016, 17:18:01 UTC
a732aea Updated `gmt` tab completion. 13 May 2016, 12:18:25 UTC
d3b5c80 Updated `genome` tab completion. 13 May 2016, 12:17:39 UTC
50e0186 Merge pull request #1420 from tmooney/clinseq_modelsummary_test_uses_test_data ClinSeq ModelSummary test uses Test Data 12 May 2016, 22:01:12 UTC
feafc43 Switch result user/input creation to __define__. Some tests run UR::Context->commit(); which doesn't work if "real" objects have FKs to __defined__ ones. This makes sure all the descendents of our defined results are themselves __defined__ at cost of requiring knowledge of the implementation details of the results themselves. 12 May 2016, 21:01:30 UTC
d264de8 Pull package name into a variable. Use G:U:T to get the data_dir. 12 May 2016, 19:59:06 UTC
1665f2c Switch test to use test data instead of a production model. 12 May 2016, 19:56:03 UTC
e58023f Add alignments to the RefAlign and RnaSeq builds in ClinSeq test data. 12 May 2016, 19:55:16 UTC
b786fe3 Remove "use" statement that precedes use_ok for same package. 12 May 2016, 19:06:48 UTC
1125441 Merge pull request #1414 from jasonwalker80/speedseq_params Add SpeedseqSv probability curves 12 May 2016, 18:19:40 UTC
96e7a19 Add param to test the semi-colon separated parsing. 12 May 2016, 17:43:42 UTC
a18ab4b Merge pull request #1413 from susannasiebert/interface_cleanup Use the subroutines in G::M::B::RunsDV2 instead of implementing our own 12 May 2016, 16:55:52 UTC
0667a17 Updated `genome` tab completion. 12 May 2016, 12:17:48 UTC
754a16a Merge pull request #1415 from susannasiebert/blessed_build New ClinSeq blessed build 11 May 2016, 20:13:21 UTC
5684469 New ClinSeq blessed build 11 May 2016, 19:39:48 UTC
28d3c86 remove inadvertent breakpoint 11 May 2016, 19:39:16 UTC
0130011 Add support for -P param to speedseq sv. cleanup the variable and method names resolving tool parameters. 11 May 2016, 19:17:28 UTC
a44e669 Clean up the snvs_annotated_variants_vcf_file since the annotated file is SomVar specific 11 May 2016, 18:40:42 UTC
d106aeb Use the subroutines in G::M::B::RunsDV2 instead of implementing our own 11 May 2016, 18:06:44 UTC
0270bce Merge pull request #1412 from jasonwalker80/vep_for_dog VEP for dog genome. 11 May 2016, 17:15:23 UTC
cfafeba Add dog reference as a valid value. 11 May 2016, 16:41:09 UTC
b776c8e Merge pull request #1406 from tmooney/remove_clinseq_originalscripts Remove ClinSeq OriginalScripts Directory 11 May 2016, 15:09:09 UTC
2706cc6 Updated `gmt` tab completion. 11 May 2016, 12:18:54 UTC
2648fd1 Updated `genome` tab completion. 11 May 2016, 12:18:11 UTC
8a9b0a7 Updated class browser cache. 11 May 2016, 12:16:37 UTC
549aab9 Remove ClinSeq-specific parts of Command::Tester (This should probably be removed completely in a new PR!) 10 May 2016, 21:39:44 UTC
a8ab88a Remove old ClinSeq "OriginalScripts" directory. 10 May 2016, 21:37:56 UTC
8882b2f Merge pull request #1392 from susannasiebert/clinseq_somatic_interface Allow ClinSeq to also use Somatic Validation models as inputs 10 May 2016, 20:16:08 UTC
562e20d Merge pull request #1405 from tmooney/copynumber_cnview_tests_use_test_cnv_data CopyNumber CnView: Use test CNV data. 10 May 2016, 20:10:40 UTC
e467d39 Merge pull request #1404 from tmooney/remove_somvar_compare_variants Remove SomticVariation Compare Variants. 10 May 2016, 20:10:30 UTC
b60bbf0 Merge pull request #1403 from tmooney/clinseq_summarizesnvs_test_uses_test_data ClinSeq SummarizeCnvs uses test data for its test. 10 May 2016, 20:10:21 UTC
88472ac Merge pull request #1402 from tmooney/converge_summarizesnvindelreport_uses_test_data ClinSeq's SummarizeSnvIndel Converge Test Uses Test Data 10 May 2016, 20:10:12 UTC
e0a15a1 Merge pull request #1401 from tmooney/cufflinksde_converge_uses_test_data ClinSeq's Cufflinks Converge uses Test Data 10 May 2016, 20:10:02 UTC
9b2af1e Merge pull request #1398 from ebelter/split-by-scaffold SX: Split sequences by ns 10 May 2016, 18:25:51 UTC
8623ddb Update test description--not from the DB anymore! 10 May 2016, 18:22:22 UTC
01d6152 Use test CNV data. 10 May 2016, 18:19:46 UTC
4bf4581 Remove SomticVariation Compare Variants. 10 May 2016, 17:51:52 UTC
17748a9 ClinSeq SummarizeCnvs uses test data for its test. 10 May 2016, 17:40:12 UTC
9702ef6 Update test to use test data instead of production data. 10 May 2016, 15:58:33 UTC
307e1cf Sort so we get a consistent output result. 10 May 2016, 15:25:52 UTC
2f72c03 Use fake builds for the test instead of relying on database data. 10 May 2016, 15:25:26 UTC
2594bc1 Update expected test data. (Now with better directory naming!) 10 May 2016, 15:15:30 UTC
d00f0ca Extract a variable for the package name. 10 May 2016, 13:13:36 UTC
85f51a4 Stop using the command we're about to "use_ok". 10 May 2016, 13:10:54 UTC
3848f82 Split qualities too 09 May 2016, 20:39:33 UTC
7559c15 Split qualities too 09 May 2016, 20:39:18 UTC
1a94725 Use subtest 09 May 2016, 20:13:58 UTC
7e78577 Use iterator style split function 09 May 2016, 20:04:02 UTC
4fd9a41 Updated `gmt` tab completion. 09 May 2016, 20:01:04 UTC
e850ab2 Updated `genome` tab completion. 09 May 2016, 19:58:39 UTC
8609ce5 Updated class browser cache. 09 May 2016, 19:52:58 UTC
7ba5aba Merge pull request #1384 from tmooney/workflowbuilder_supports_nested_xml WorkflowBuilder supports references to other XML files 09 May 2016, 18:20:06 UTC
6fd1351 Use create temp dir 09 May 2016, 17:01:57 UTC
171b573 Split By Ns: immediately write split seqs 09 May 2016, 16:50:53 UTC
88c682b Update test db 09 May 2016, 16:42:04 UTC
098408f Fix a few more spots where we used to get properties via the model instead of the build 09 May 2016, 16:38:23 UTC
2b71455 Use fatal_message instead of die error_message 09 May 2016, 16:37:58 UTC
d794e97 Merge pull request #1387 from tmooney/remove_weird_move_alignment_directory_command Remove obsolete "MoveAlignmentDirectory" command. 09 May 2016, 13:35:44 UTC
e4ecbd2 Merge pull request #1383 from tmooney/genotypemicroarray_test_doesnt_use_workflowsimple Remove unused include in GenotypeMicroarray.t 09 May 2016, 13:35:14 UTC
47e0157 Merge pull request #1382 from tmooney/remove_blastx_parallel Remove "parallel" blastx tool. 09 May 2016, 13:35:00 UTC
a79e2b7 Merge pull request #1360 from tmooney/remove_parallel_annotator Remove Parallel Annotator. 09 May 2016, 13:34:19 UTC
645534f Merge pull request #1359 from tmooney/remove_parallel_refcov Remove old "parallel ref-cov". 09 May 2016, 13:34:04 UTC
a6bfaf0 Merge pull request #1358 from tmooney/safe_vcf_merge_uses_workflowbuilder Use WorkflowBuilder to make SafeVCFMerge workflow. 09 May 2016, 13:33:43 UTC
00c4fc6 Merge pull request #1395 from tmooney/vep_typos_fo_potput Fix some typos in documentation of Ensembl annotation runner. 09 May 2016, 13:33:23 UTC
5a0821b Run AnnotateSnvsVcf step as part of ClinSeq workflow 06 May 2016, 18:36:29 UTC
9c002ce Have AnnotateSnvsVcf take a somatic build as an input, not the vcf 06 May 2016, 15:24:46 UTC
6688d36 Revert "Rename class" This reverts commit 13d3b4b2e6bbb3397b4ed89a0d8d8724817fdd62. 06 May 2016, 14:47:00 UTC
74d7019 Merge branch 'master' of https://github.com/genome/genome into clinseq_somatic_interface 06 May 2016, 14:21:14 UTC
554e42d Merge pull request #1397 from susannasiebert/vcf_annotate_sr A new ClinSeq command and software result for annotating snvs vcf file 06 May 2016, 14:20:32 UTC
b446a14 Split by this many or more ns 05 May 2016, 21:47:01 UTC
b731655 Split sequences by ns 05 May 2016, 21:24:12 UTC
13d3b4b Rename class 05 May 2016, 19:49:27 UTC
e0974dd Merge pull request #1334 from tmooney/instrumentdata_import_uses_workflowbuilder_inline Use the new execute_inline for DAG instead of relying on Workflow. 05 May 2016, 19:42:15 UTC
8b1eb8c Merge pull request #1324 from tmooney/sata420_isnt_real Remove references to sata420. 05 May 2016, 19:41:52 UTC
05c3504 Merge pull request #1317 from tmooney/ptero_execution_info A Command to Get Information about a PTero Execution. 05 May 2016, 19:41:35 UTC
009140b Merge pull request #1389 from jasonwalker80/manta_dv2 Manta DV2 Detector 05 May 2016, 19:37:19 UTC
b8403e1 Merge pull request #1300 from tmooney/ssg_can_symlink_results SingleSampleGenotype Can Be Checked Out; Uses Said Checkout for Diffs 05 May 2016, 19:21:26 UTC
fe5f271 Make info_fields optional 05 May 2016, 18:49:01 UTC
3703f97 Name the output file the same as the input file annotate is an overloaded term 05 May 2016, 18:17:42 UTC
4a753da ClinSeq command and software result for annotating snvs vcf file 05 May 2016, 15:11:14 UTC
ccf71f5 Fix bug in the use_bgzip option in the joinx vcf-annotate wrapper 05 May 2016, 15:10:38 UTC
7665def Merge pull request #1396 from sleongmgi/sleong-add-message-to-test put an message because it might cause error if it is only one test. 04 May 2016, 18:05:35 UTC
a2c3751 remove the comment and add the intention to the old comment. 04 May 2016, 17:55:02 UTC
0abb090 put an message because it might cause error if it is only one test. 04 May 2016, 17:20:54 UTC
51b108f Use Path::Class to resolve relative path rather than regex. 04 May 2016, 15:03:32 UTC
6cd45bf s/fo/of/ and s/potput/output/. 03 May 2016, 21:41:56 UTC
f7b69e7 Update test db 03 May 2016, 18:16:40 UTC
fcb067d Rework how microarray builds are retrieved from ClinSeq builds 03 May 2016, 17:47:15 UTC
48cdfce Use fatal_message 03 May 2016, 17:47:15 UTC
8bd2611 Use SomaticInterface 03 May 2016, 17:47:14 UTC
0734d88 Fix typos 03 May 2016, 17:47:14 UTC
92dddf4 Fix logic to determine individual 03 May 2016, 17:47:14 UTC
8432277 clean up _input_models and input_builds subroutines 03 May 2016, 17:47:13 UTC
8311ba2 use File::Spec->join 03 May 2016, 17:47:13 UTC
dcb72a7 Merge pull request #1393 from tmooney/quiet_ssg_listoutputfiles_single_use_warning Quiet variable use warning in SSG ListOutputFiles test. 03 May 2016, 13:58:47 UTC
aacd306 Merge pull request #1394 from sleongmgi/sleong-redirect-standard-out-to-dev-null Redirect the standard output and error to the /dev/null. 03 May 2016, 13:58:33 UTC
a0e3287 Redirect the standard output and error to the /dev/null. Otherwise, the standard output will interfere with the TAP output. 03 May 2016, 12:32:18 UTC
6e8e57f Move the substitution into the if condition since it returns true if there is a match. 02 May 2016, 21:36:05 UTC
542ecfe spelling correction 02 May 2016, 19:09:52 UTC
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