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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
a49edfe Nathan Nutter 04 December 2012, 17:34:50 UTC improve debug message 04 December 2012, 17:34:50 UTC
912644d Nathan Nutter 04 December 2012, 17:34:38 UTC invert conditional 04 December 2012, 17:34:38 UTC
896e2c6 Nathan Nutter 04 December 2012, 17:33:56 UTC move vcf_version into the get 04 December 2012, 17:33:56 UTC
9ee735f Charles Lu 04 December 2012, 16:30:55 UTC fixed a bug so that RSID is matched to the right variant allele 04 December 2012, 16:30:55 UTC
04673a5 Thomas Mooney 04 December 2012, 16:22:58 UTC Don't include inputs from the helper in type-specific parameters. This fixes model definitions broken by making processing profile an input in 8fb1465afa56aafe2ab6a0baa8152dd4f3f51fd7. 04 December 2012, 16:22:58 UTC
8c7a264 Obi Griffith 04 December 2012, 04:42:01 UTC added blacklist 04 December 2012, 04:42:01 UTC
cf2d598 Obi Griffith 04 December 2012, 04:39:56 UTC moved Uniprot to Entrez sub to Base.pm 04 December 2012, 04:39:56 UTC
a15387a Malachi Griffith 04 December 2012, 03:39:08 UTC Fix clin-seq update-analysis test and minor update to Main.pm 04 December 2012, 03:39:08 UTC
5f77a9e Malachi Griffith 04 December 2012, 01:12:09 UTC Cosmetic update to cn-view 04 December 2012, 01:12:09 UTC
646dd7f Nathan Nutter 04 December 2012, 01:10:24 UTC remove test case for behavior that was removed 04 December 2012, 01:10:30 UTC
db86b3e Malachi Griffith 04 December 2012, 00:38:38 UTC Merge branch 'master' of ssh://git/srv/git/genome 04 December 2012, 00:38:38 UTC
6bc1de0 Nathan Nutter 04 December 2012, 00:10:24 UTC remove check that prevents valid, relative link 04 December 2012, 00:11:39 UTC
bef7f0b Nathan Nutter 04 December 2012, 00:02:38 UTC fix typo and hide option 04 December 2012, 00:11:38 UTC
6bb2dbf Nathan Nutter 03 December 2012, 23:52:12 UTC add blacklisted segments to view 04 December 2012, 00:11:38 UTC
acbf79c Nathan Nutter 03 December 2012, 23:18:05 UTC add ability to blacklist segments - allow segments to be blacklisted by adding one or more blacklisted_segments attributes - make get_segments default to only return non-blacklisted segments but allow overriding with method option 04 December 2012, 00:11:38 UTC
a4fbd23 Nathan Nutter 03 December 2012, 23:04:51 UTC whitespace 04 December 2012, 00:11:37 UTC
b57f7b0 Nathan Nutter 03 December 2012, 22:38:58 UTC whitespace 04 December 2012, 00:11:37 UTC
5ca58b5 Nathan Nutter 03 December 2012, 22:19:19 UTC whitespace 04 December 2012, 00:11:36 UTC
d0b6a67 Eddie Belter 03 December 2012, 22:32:53 UTC Misc update: add has_failed method 03 December 2012, 22:32:53 UTC
a416111 Eddie Belter 03 December 2012, 22:24:44 UTC Reconcile udpate: tweak report 03 December 2012, 22:24:54 UTC
d7e178e Eddie Belter 03 December 2012, 22:23:26 UTC Multi misc update: check return of genome entitty params 03 December 2012, 22:24:54 UTC
e250c8e Eddie Belter 03 December 2012, 22:22:49 UTC Misc update: results are now PASS, FAIL and SKIP; add desc to status 03 December 2012, 22:24:53 UTC
1bd965f Charles Lu 03 December 2012, 21:41:27 UTC Merge branch 'master' of ssh://git/srv/git/genome 03 December 2012, 21:41:27 UTC
4a714b4 Charles Lu 03 December 2012, 21:41:19 UTC added tool to add RSid to annotation file 03 December 2012, 21:41:19 UTC
d50e366 Nathan Nutter 03 December 2012, 21:34:04 UTC since log_file is optional don't expect it 03 December 2012, 21:34:04 UTC
7198de0 Nathan Nutter 03 December 2012, 21:26:45 UTC fix "false positives" in model-summary 03 December 2012, 21:26:53 UTC
1abf06a Nathan Nutter 03 December 2012, 21:25:48 UTC hide summary report 03 December 2012, 21:26:52 UTC
b6da844 Nathan Nutter 03 December 2012, 21:25:28 UTC add option to hide summary report 03 December 2012, 21:26:52 UTC
0d4b17b Nathan Nutter 03 December 2012, 20:47:13 UTC make relative symlink if possible If build's data directory is moved because allocation is moved or unarchived then a relative symlink will survive. 03 December 2012, 21:26:52 UTC
5533d1b Nathan Nutter 03 December 2012, 19:56:39 UTC moved to jenkins repo 03 December 2012, 21:26:51 UTC
6c5e054 APipe Tester 03 December 2012, 19:57:41 UTC updated jenkins submodule to 255d4fd 03 December 2012, 19:57:41 UTC
c55e5b5 dmorton 03 December 2012, 19:51:04 UTC Made tool to help back-fill DV2 vcf results They were not saving their results in the DB since they had 'has' instead of 'has_param' or 'has_input'. Gabe and I worked on a method to determine the missing information from related software-results. 03 December 2012, 19:52:58 UTC
7e21932 APipe Tester 03 December 2012, 19:47:33 UTC updated workflow submodule to ca05ba8 03 December 2012, 19:47:33 UTC
abbf16c Malachi Griffith 03 December 2012, 17:48:19 UTC Merge branch 'master' of ssh://git/srv/git/genome 03 December 2012, 17:48:19 UTC
015d05f Malachi Griffith 03 December 2012, 17:44:51 UTC Updates to how cn-view in called in clin-seq main to accommodate updates to cn-view 03 December 2012, 17:44:51 UTC
c025c98 Scott Smith 03 December 2012, 05:28:47 UTC Add to clinseq: Summarize Builds is now in the workflow. Also fixed a bug with passing params to SummarizeSVs. And turned off the "clean" option since it doesn't work nicely with parallelization. 03 December 2012, 05:28:47 UTC
56c2f01 Malachi Griffith 03 December 2012, 04:59:18 UTC Major refactor of CnView tool. Added transcript level results and improved run time 03 December 2012, 04:59:18 UTC
44973b5 Gabriel Sanderson 30 November 2012, 22:32:05 UTC Merge branch 'master' into gb_master 30 November 2012, 22:32:05 UTC
e7c6330 Gabriel Sanderson 30 November 2012, 22:31:50 UTC Added more files to files ignored by diff 30 November 2012, 22:31:55 UTC
815ecc1 APipe Tester 30 November 2012, 21:41:48 UTC updated ur submodule to 2d5fcac 30 November 2012, 21:41:48 UTC
ff0607a Gabriel Sanderson 30 November 2012, 20:48:43 UTC Merge branch 'master' into gb_master 30 November 2012, 20:48:43 UTC
de3edd5 Gabriel Sanderson 30 November 2012, 20:47:25 UTC Added to files ignored by diff 30 November 2012, 20:47:36 UTC
ae3b7b5 Nathan Nutter 30 November 2012, 20:07:17 UTC improve error message when page fails to load - set email address to apipe-support@rt.gsc.wustl.edu - include URL in body of email (if mail link is used) - I have no clue how to test this... 30 November 2012, 20:08:23 UTC
3e2dd2e Scott Smith 30 November 2012, 19:55:53 UTC Merge branch 'master' of ssh://git/srv/git/genome 30 November 2012, 19:55:53 UTC
65a5b13 Scott Smith 30 November 2012, 19:53:46 UTC Improved clinseq parallelization. The ClinSeq (to be renamed) pipeline now launches SummarizeSvs and SummarizeCnvs in parallel, as independent workflow operations, and uses a dynamically generated workflow internally instead of the _execute_build API. The Main step now has two outputs, one for the input directory of each of the subsequent steps. The Main step now does more on a "dry run" execution, testing the lighter-weight parts of main inside of ClinSeq.t. The "dry run" version of the pipeline still skips the rest of the worflow so that those steps do not need to have special "do nothing" logic. This commit depends on an update to Workflow which ensures that the Command adaptor (Workflow::OperationType::Command) treats both params and inputs as operation inputs. 30 November 2012, 19:53:46 UTC
0619f94 dmorton 30 November 2012, 16:19:12 UTC Fix typo 30 November 2012, 19:32:48 UTC
9ae00ee dmorton 28 November 2012, 18:18:42 UTC Fix typo in calling UR::Context function. 30 November 2012, 19:32:48 UTC
236fbe3 APipe Tester 30 November 2012, 18:41:52 UTC updated jenkins submodule to 3256f90 30 November 2012, 18:41:52 UTC
7ab0e03 Scott Smith 30 November 2012, 18:26:42 UTC Merge branch 'master' of ssh://git/srv/git/genome 30 November 2012, 18:26:42 UTC
a49b984 Scott Smith 30 November 2012, 18:26:31 UTC updated to be robust vs Workflow fixes for is_param 30 November 2012, 18:26:31 UTC
1bddaf9 Mark Burnett 30 November 2012, 17:53:51 UTC add *_id params to DV2:Result:Vcf:Combine 30 November 2012, 17:53:51 UTC
ed0782d Mark Burnett 30 November 2012, 17:52:48 UTC make sure get_or_create complains with extra inputs 30 November 2012, 17:52:48 UTC
61fa1c9 apregier 30 November 2012, 16:16:48 UTC Merge branch 'fix' into gb_master 30 November 2012, 16:16:48 UTC
92f6766 apregier 30 November 2012, 16:13:10 UTC Fix typo 30 November 2012, 16:13:10 UTC
d928e84 apregier 30 November 2012, 16:11:51 UTC Add a command to remove test name from software results 30 November 2012, 16:12:02 UTC
1a06162 Mark Burnett 30 November 2012, 16:05:38 UTC make SR set-test-name accept multiple software results 30 November 2012, 16:07:42 UTC
941232a apregier 30 November 2012, 16:02:18 UTC Merge branch 'fix' into gb_master 30 November 2012, 16:02:18 UTC
72e4353 apregier 27 November 2012, 17:53:50 UTC Add Multi file to default dbsnp import list 30 November 2012, 16:01:48 UTC
86c6878 Mark Burnett 30 November 2012, 15:37:25 UTC update SR fill lookup_hash command 30 November 2012, 15:37:25 UTC
3dbd732 APipe Tester 30 November 2012, 00:14:26 UTC updated ur submodule to 0fe035f 30 November 2012, 00:14:26 UTC
8b6b36f APipe Tester 29 November 2012, 23:25:15 UTC updated workflow submodule to bdf89b4 29 November 2012, 23:25:15 UTC
c806871 Malachi Griffith 29 November 2012, 23:07:42 UTC Update clin-seq get-bam-read-counts test to deal with modified format of input file 29 November 2012, 23:07:42 UTC
665a85a APipe Tester 29 November 2012, 23:01:18 UTC updated workflow submodule to 25a4c35 29 November 2012, 23:01:18 UTC
c5a8f5c APipe Tester 29 November 2012, 22:46:17 UTC updated workflow submodule to e6808bf 29 November 2012, 22:46:17 UTC
96d0b06 Malachi Griffith 29 November 2012, 22:16:39 UTC Hotfix for clin-seq update analysis 29 November 2012, 22:16:39 UTC
e73b343 Gabriel Sanderson 29 November 2012, 21:23:54 UTC Merge branch 'master' into gb_master 29 November 2012, 21:23:54 UTC
af72f61 Gabriel Sanderson 29 November 2012, 21:23:45 UTC Fixed another potential uninitialized value warning 29 November 2012, 21:23:45 UTC
ce2101f Gabriel Sanderson 29 November 2012, 21:18:08 UTC Merge branch 'master' into gb_master 29 November 2012, 21:18:08 UTC
69fd692 Gabriel Sanderson 29 November 2012, 21:17:55 UTC Fixed a warning that occurred many times if FT was not defined. 29 November 2012, 21:18:04 UTC
4f6081e Gabriel Sanderson 29 November 2012, 21:11:39 UTC Merge branch 'vcfresult' into gb_master 29 November 2012, 21:11:39 UTC
b5ed18e Gabriel Sanderson 29 November 2012, 21:10:55 UTC Fix Vcf filter and combine results to save their properties as inputs/params. 29 November 2012, 21:11:24 UTC
dbcdb48 APipe Tester 29 November 2012, 21:09:46 UTC updated ur submodule to d2de503 29 November 2012, 21:09:46 UTC
0e145bb Thomas Mooney 29 November 2012, 20:02:13 UTC Just make it optional so we don't try to save NULL to the db. 29 November 2012, 20:02:13 UTC
ad462f6 Mark Burnett 29 November 2012, 19:36:00 UTC change Disk::Allocation to not rely on perl 5.10 29 November 2012, 19:36:00 UTC
2016dcf Mark Burnett 29 November 2012, 19:24:31 UTC Db:E:AnnotationStructuresm now updates lookup_hash when it changes test_name 29 November 2012, 19:26:33 UTC
1ef2954 Mark Burnett 29 November 2012, 19:24:00 UTC add remove_test_name function to SoftwareResult 29 November 2012, 19:26:33 UTC
382ac2e APipe Tester 29 November 2012, 18:59:29 UTC Merge remote-tracking branch 'origin/master' 29 November 2012, 18:59:29 UTC
4dc5046 Eddie Belter 29 November 2012, 18:19:07 UTC Misc update: improve test for SKIPs; add site tgi class method 29 November 2012, 18:19:13 UTC
9facbfc Mark Burnett 29 November 2012, 17:54:14 UTC disable Model/ClinSeq/Command/GetBamReadCounts.t This test was blocking us from deploying an important SoftwareResult change. It appears that the test data were not updated when code was changed. 29 November 2012, 17:54:14 UTC
94564f3 Mark Burnett 29 November 2012, 17:34:07 UTC fix DbSnpConcordance.t 29 November 2012, 17:34:07 UTC
26ab9ab Mark Burnett 29 November 2012, 17:28:43 UTC fix chimerascan result test 29 November 2012, 17:29:26 UTC
d71ebac Adam Coffman 29 November 2012, 17:20:11 UTC Revert "Override test_name accessor instead of introducing new set method" __ syntax doesn't seem to work for delegated property accessors This reverts commit 0d3b3c3d22c803071c83ae4c53f7988e1d9144f8. 29 November 2012, 17:20:11 UTC
0d3b3c3 Adam Coffman 29 November 2012, 17:01:17 UTC Override test_name accessor instead of introducing new set method 29 November 2012, 17:01:17 UTC
01f3582 Thomas Mooney 29 November 2012, 16:35:06 UTC Fixes for the combine test: actually set the inputs on the VCF results *This changes the diff of the generated VCF for one test, so the data has been updated as well. 29 November 2012, 16:35:06 UTC
2141de7 Mark Burnett 29 November 2012, 16:33:32 UTC add command: 'genome software-result set-test-name' 29 November 2012, 16:33:32 UTC
84b91d5 Mark Burnett 29 November 2012, 16:25:20 UTC decrease chunk size for FillLookupHashes 29 November 2012, 16:25:20 UTC
15f11bf Mark Burnett 29 November 2012, 15:56:16 UTC add set_test_name to SoftwareResult 29 November 2012, 15:56:16 UTC
ac65dc3 Mark Burnett 29 November 2012, 15:30:23 UTC make sample optional in DV2:Result:Manual 29 November 2012, 15:30:23 UTC
f09f95e Mark Burnett 29 November 2012, 15:23:34 UTC Merge remote-tracking branch 'origin/master' into software_result_hashing 29 November 2012, 15:23:34 UTC
0a0ead9 Mark Burnett 29 November 2012, 15:19:43 UTC change expected test count for ID:AR:Bwa 29 November 2012, 15:21:23 UTC
f52a17f Mark Burnett 29 November 2012, 15:17:43 UTC make roi_track_name optional in ID:AR:CoverageStats 29 November 2012, 15:21:23 UTC
7355fda Thomas Mooney 29 November 2012, 15:19:32 UTC The aligned_reads_sample isn't needed for combine VCFs--it comes from inputs. Since it's required in the base class, just give it a default value to satisfy existence. 29 November 2012, 15:19:32 UTC
6e42a38 Mark Burnett 29 November 2012, 15:03:09 UTC fix SR/Stagable.t 29 November 2012, 15:03:09 UTC
081d802 Mark Burnett 29 November 2012, 14:54:14 UTC fix expected test count in ID:AR:Bsmap.t 29 November 2012, 14:54:14 UTC
a644a4b Thomas Mooney 29 November 2012, 14:09:38 UTC No combine results appear to have "version" set, so make it optional. 29 November 2012, 14:09:38 UTC
9b1618b Malachi Griffith 29 November 2012, 05:51:39 UTC Fixed bug with check of instrument data type checking in clin-seq update-analysis 29 November 2012, 05:51:39 UTC
9eeb023 Malachi Griffith 29 November 2012, 05:29:16 UTC Major clean-up of CnView tool in advance of further refactor 29 November 2012, 05:29:16 UTC
3bd0b96 Scott Smith 29 November 2012, 05:25:55 UTC fixed bug in which genome model input update would not allow a value to be set to zero 29 November 2012, 05:25:55 UTC
bd465c3 Mark Burnett 29 November 2012, 00:46:20 UTC Merge branch 'software_result_hashing' of ssh://git/srv/git/genome into software_result_hashing 29 November 2012, 00:46:20 UTC
e6e3a4a Mark Burnett 29 November 2012, 00:45:19 UTC add lookup_hash to stagable SR test 29 November 2012, 00:45:19 UTC
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