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23 March 2024, 19:04:16 UTC
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Revision Author Date Message Commit Date
68562f7 Thomas Mooney 11 March 2014, 18:47:02 UTC Add accessors to get to the analysis projects. 11 March 2014, 18:47:02 UTC
f0e9b4c Thomas Mooney 11 March 2014, 18:13:10 UTC Tag the new db table 11 March 2014, 18:34:56 UTC
2d16fa9 Thomas Mooney 11 March 2014, 18:06:16 UTC New bridge entity explicitly linking APs and models 11 March 2014, 18:34:56 UTC
559cb74 Nathaniel Nutter 11 March 2014, 17:48:31 UTC change status_message to debug_message Since the content of the message could be interpreted as an error/warning rather than just a informational I am changing this to a debug message. 11 March 2014, 18:08:24 UTC
c4d2a88 Craig Pohl 11 March 2014, 18:04:44 UTC Merge branch 'ber_dev' 11 March 2014, 18:04:44 UTC
ef54efe Craig Pohl 11 March 2014, 18:03:59 UTC stomping on ajia dev with my changes 11 March 2014, 18:03:59 UTC
3222854 Nathaniel Nutter 11 March 2014, 17:41:33 UTC refactoring to allow memory limits to be overrode for FastQC * copy fastqc argument parsing to allow override * switch maximum_memory to be in MB instead of GB * -cp option and value shouldn't be split apart * split across multiple lines 11 March 2014, 17:41:33 UTC
6d35c72 Nathaniel Nutter 10 March 2014, 23:27:46 UTC copy fastqc argument parsing to allow override 11 March 2014, 17:41:07 UTC
51a4d27 Nathaniel Nutter 10 March 2014, 23:23:51 UTC switch maximum_memory to be in MB instead of GB Nowhere had used it yet and FastQC needs MB level granularity since the default is 250 MB and is supposed to scale with threads. 11 March 2014, 17:41:06 UTC
b2db5a1 Nathaniel Nutter 10 March 2014, 23:07:22 UTC -cp option and value shouldn't be split apart 11 March 2014, 17:41:05 UTC
2f97386 Nathaniel Nutter 10 March 2014, 22:08:26 UTC split across multiple lines 11 March 2014, 17:41:05 UTC
e50bd0a apregier 11 March 2014, 15:24:05 UTC Merge branch 'my_annotation' into gb_master 11 March 2014, 15:24:05 UTC
e395f48 apregier 11 March 2014, 15:17:04 UTC Analysis project is optional 11 March 2014, 15:18:34 UTC
a9faf76 Thomas Mooney 11 March 2014, 13:37:06 UTC spelling: anlysis => analysis 11 March 2014, 13:37:06 UTC
bda0463 APipe Tester 11 March 2014, 12:17:17 UTC Updated `gmt` tab completion. 11 March 2014, 12:17:17 UTC
4f89293 APipe Tester 11 March 2014, 12:16:35 UTC Updated `genome` tab completion. 11 March 2014, 12:16:35 UTC
0dc3e72 Nathaniel Nutter 10 March 2014, 23:48:09 UTC fix typo 10 March 2014, 23:48:09 UTC
e2cf945 Adam Coffman 10 March 2014, 21:31:12 UTC Round default archive after time to nearest 00:00:00 We had a couple of DST related failures where this value was set to a time that didn't exist. This will avoid that issue, though will still be vulnerable to leap-seconds. We deem that to be fine for now. 10 March 2014, 21:31:12 UTC
dd7cb34 Nathaniel Nutter 10 March 2014, 20:50:13 UTC lock in result_version => 1 We recently updated the default result_version to 2 which cause this to no longer shortcut which increased the run time from 5 seconds to >30 minutes. 10 March 2014, 20:50:13 UTC
57fcd92 Nathaniel Nutter 10 March 2014, 20:08:29 UTC update expected output due to new instrument data This test uses production data (TST1) and it looks like a new instrument data came in so I updated the expected output. diff -ur /gscmnt/gc13003/info/test_suite_data/Genome-InstrumentData-Command-Export-Samplesheet/2014-02-25/expected-output/ss.csv /gscmnt/gc13003/info/test_suite_data/Genome-InstrumentData-Command-Export-Samplesheet/2014-03-10/expected-output/ss.csv --- /gscmnt/gc13003/info/test_suite_data/Genome-InstrumentData-Command-Export-Samplesheet/2014-02-25/expected-output/ss.csv 2014-02-25 10:41:28.458286000 -0600 +++ /gscmnt/gc13003/info/test_suite_data/Genome-InstrumentData-Command-Export-Samplesheet/2014-03-10/expected-output/ss.csv 2014-03-10 14:58:41.827292000 -0500 @@ -14,3 +14,4 @@ C1TD1ACXX,8,ACAGTG,,human,9606,Eukaryota,3200000000,H_NJ-HCC1395,TST1,Caucasian,female,H_NJ-HCC1395-HCC1395_RNA,tumor,primary,,HCC1395_RNA,rna,epithelial,Pooled_RNA_2891007020-mRNA2-cDNA-1-lig1-lib1,264,383,Illumina Library Construction,Paired,CASAVA-1.8.2,156248832,100,100,4.61,2891354555,2891075264,2889953342,2889953340,1653198737 C2DBEACXX,3,,,human,9606,Eukaryota,3200000000,H_NJ-HCC1395,TST1,Caucasian,female,H_NJ-HCC1395-HCC1395_BL_RNA,normal,primary,,HCC1395 BL_RNA,rna,b lymphoblast,Pooled_RNA_2891006726-mR1-cD1-lg1-lib1,364,483,Illumina Library Construction,Paired,CASAVA-1.8.2,170049877,100,100,,2893585922,2893186767,2889953341,2889953340,1653198737 A7A98,1,,WO2841453 pooled probes + WO2841718 pooled probes,human,9606,Eukaryota,3200000000,H_NJ-HCC1395,TST1,Caucasian,female,H_NJ-HCC1395-HCC1395_BL_RNA,normal,primary,,HCC1395 BL_RNA,rna,b lymphoblast,Pooled_RNA_2891006726-mR1-cD1-lg2-lib1,253,372,Illumina Library Construction,Paired,CASAVA-1.8.2,13994180,250,250,10.17,2893874080,2893843645,2889953341,2889953340,1653198737 +A7A3G,1,,WO2841453 pooled probes + WO2841718 pooled probes,human,9606,Eukaryota,3200000000,H_NJ-HCC1395,TST1,Caucasian,female,H_NJ-HCC1395-HCC1395_RNA,tumor,primary,,HCC1395_RNA,rna,epithelial,Pooled_RNA_2891007020-mRNA2-cDNA-1-lg1-lib1,203,322,Illumina Library Construction,Paired,CASAVA-1.8.2,5101654,250,250,10.23,2893908598,2893904253,2889953342,2889953340,1653198737 10 March 2014, 20:08:29 UTC
e2decf3 Jim Weible 10 March 2014, 19:12:01 UTC remove useless method 10 March 2014, 19:12:01 UTC
d80778b Jim Weible 06 March 2014, 16:40:13 UTC remove the create functionality from get_or_create_lane_qc_models. This behavior was deprecated by AP Config, which is now responsible for creating lane_qc models. See AUE-190 for details 10 March 2014, 18:21:07 UTC
ca8dcb5 Nathaniel Nutter 10 March 2014, 17:58:30 UTC Htseq::Count v2 * bump default version of Htseq::Count to v2 * Genome::Model::Tools::Htseq::Count v2 * extract method _htseq_stranded_param 10 March 2014, 17:58:30 UTC
02f9f72 Nathaniel Nutter 10 March 2014, 17:56:24 UTC bump default version of Htseq::Count to v2 Since v1 produces bad results the default should be bumped to v2. 10 March 2014, 17:57:06 UTC
475137f Nathaniel Nutter 07 March 2014, 21:41:48 UTC Genome::Model::Tools::Htseq::Count v2 Fixes bug reported in RT/98157 and defined new result as v2. The only change is in the _htseq_stranded_param so methods version by Genome::Command::WithSavedResults are just aliased to v1. 10 March 2014, 17:57:06 UTC
88ecd48 Nathaniel Nutter 07 March 2014, 21:34:52 UTC extract method _htseq_stranded_param 10 March 2014, 17:57:05 UTC
b7a4f1a Nathaniel Nutter 10 March 2014, 17:50:30 UTC refactoring of FeatureList while working on RT/98143 * pinch: show line number and content when track name is unknown skip genome browser annotation lines extract duplicated bed entry parsing code into sub 10 March 2014, 17:50:30 UTC
419ec7d Nathaniel Nutter 07 March 2014, 20:27:20 UTC show line number and content when track name is unknown 10 March 2014, 17:49:18 UTC
1fd4a8d Nathaniel Nutter 07 March 2014, 20:25:59 UTC skip genome browser annotation lines The BED format as described on the UCSC has examples that contain Genome Browser annotation lines starting with 'browser' so it seems like we should just skip them (or maybe print them). 10 March 2014, 17:49:18 UTC
7ee3028 Nathaniel Nutter 07 March 2014, 20:18:39 UTC extract duplicated bed entry parsing code into sub 10 March 2014, 17:49:17 UTC
3070a76 Thomas Mooney 10 March 2014, 14:41:41 UTC Remove outdated comments. Even if they are still relevant, shellcmd() isn't in this file. 10 March 2014, 14:41:41 UTC
720cebf APipe Tester 08 March 2014, 13:17:17 UTC Updated `genome` tab completion. 08 March 2014, 13:17:17 UTC
28e2220 apregier 07 March 2014, 20:32:18 UTC Merge branch 'my_annotation' into gb_master 07 March 2014, 20:32:18 UTC
9dd8de3 apregier 07 March 2014, 20:30:45 UTC Added new processing profile parameters to import/export test 07 March 2014, 20:31:21 UTC
75e24f3 dmorton 07 March 2014, 18:54:00 UTC Bugfix: Missed a call to _capture 07 March 2014, 18:54:00 UTC
fe7245c dmorton 07 March 2014, 17:04:28 UTC Bugfix: Name of function on FeatureList changed 07 March 2014, 17:04:28 UTC
700188a dmorton 07 March 2014, 17:02:17 UTC Move lazy-loading of IPC::Sysem::Simple into Genome::Sys 07 March 2014, 17:04:08 UTC
9276a15 Anthony Brummett 05 March 2014, 21:58:47 UTC Tighten up the new Nessy locks When locking, get the Nessy lock first, then the file-based lock The Nessy lock adapter now understands the 'wait_on_self', 'block_sleep' and 'max_try' options. lock_resource and unlock_resource generate error_message()s when unexpected things happen, like if we can get a Nessy lock but not a file-based lock. 07 March 2014, 14:34:25 UTC
17085ae Anthony Brummett 27 February 2014, 20:28:12 UTC Hook into Nessy for locking Use the Nessy locking server if the env var GENOME_NESSY_SERVER is set. The existing disk-based locks are still used primarily. When the old-style lock succeeds, then it calls the equivalent Nessy lock method. 07 March 2014, 14:34:24 UTC
58d9ab9 Anthony Brummett 04 March 2014, 20:03:51 UTC Extract methods to parse args and handle the meat of file-based locking 07 March 2014, 14:34:23 UTC
f99d83e Susanna Siebert 06 March 2014, 18:47:59 UTC restrict_to_target_regions and target_regions also need to be processing profile params 07 March 2014, 14:11:27 UTC
06757a9 APipe Tester 07 March 2014, 14:00:07 UTC updated workflow submodule to 1951cac 07 March 2014, 14:00:07 UTC
873de14 APipe Tester 07 March 2014, 13:17:36 UTC Updated `gmt` tab completion. 07 March 2014, 13:17:36 UTC
4d00472 APipe Tester 07 March 2014, 13:16:51 UTC Updated `genome` tab completion. 07 March 2014, 13:16:51 UTC
4aaacb7 APipe Tester 07 March 2014, 13:15:14 UTC Updated class browser cache. 07 March 2014, 13:15:14 UTC
65a7ce7 Kyung Kim 07 March 2014, 04:16:52 UTC Tool to filter duplicate sequences in reads 07 March 2014, 04:16:52 UTC
36feea3 Dave Larson 07 March 2014, 03:50:44 UTC add a little bit of feedback. 07 March 2014, 03:50:50 UTC
b00be1c Avinash Ramu 06 March 2014, 23:58:18 UTC don't use hard-coded paths for db's The files required for annotation are accessed using a Genome::Db method. 06 March 2014, 23:58:18 UTC
ef4e8c8 APipe Tester 06 March 2014, 23:15:15 UTC updated workflow submodule to c8fb4b2 06 March 2014, 23:15:15 UTC
f851937 apregier 06 March 2014, 23:14:46 UTC Merge branch 'my_annotation' into gb_master 06 March 2014, 23:14:46 UTC
506e425 apregier 06 March 2014, 23:09:31 UTC Make analysis-project optional for id import 06 March 2014, 23:10:08 UTC
7a1d43a apregier 06 March 2014, 23:08:16 UTC New nomenclature 06 March 2014, 23:10:05 UTC
97dcf3b Gabriel Sanderson 06 March 2014, 22:47:12 UTC Fixed a typo in the grep. Use capture instead of backticks to make sure it runs. Test it. 06 March 2014, 22:47:20 UTC
f4aa19f dmorton 06 March 2014, 22:25:12 UTC Lean on new FeatureList functionality in 'gmt vcf cross-sample' 06 March 2014, 22:46:30 UTC
b65a56c dmorton 06 March 2014, 21:24:26 UTC Lean on new FeatureList functionality in CCSVCF 06 March 2014, 22:46:30 UTC
58f1400 APipe Tester 06 March 2014, 22:33:56 UTC updated jenkins submodule to 5e98e09 06 March 2014, 22:33:56 UTC
3afeb1c Alexander Jia 06 March 2014, 22:18:48 UTC Added Ber.t 06 March 2014, 22:18:48 UTC
335e5c6 Gabriel Sanderson 06 March 2014, 21:51:46 UTC Added resolve_roi_for_reference, which checks references before converting the bed file. Also do a basic check for "chr" chromosomes if they do not belong. 06 March 2014, 21:58:14 UTC
c57c419 Gabriel Sanderson 06 March 2014, 20:36:18 UTC target_bed checks to make sure it exists when accessed 06 March 2014, 21:58:13 UTC
1702189 Gabriel Sanderson 06 March 2014, 20:15:49 UTC Removed caching -- using software results now. 06 March 2014, 21:58:12 UTC
7b18010 Gabriel Sanderson 06 March 2014, 20:13:20 UTC Remove old TODO 06 March 2014, 21:58:10 UTC
efbbf50 Gabriel Sanderson 06 March 2014, 20:12:28 UTC Start using ConvertedBedResult instead of directly calling convert_bed 06 March 2014, 21:58:08 UTC
84d56e0 Gabriel Sanderson 06 March 2014, 02:11:32 UTC Added ConvertedBedResult to act as a software result for feature list bed files, once they are converted to another reference sequence. 06 March 2014, 21:58:06 UTC
2c7ca6a Thomas Mooney 06 March 2014, 20:28:30 UTC Fix typo: symlinke => symlink. 06 March 2014, 20:28:30 UTC
c844d7e dmorton 06 March 2014, 19:25:42 UTC remove die condition in vcf Backfill When we create vcf files from mpileup (in dv2) the converter does not put in a AD field and always leaves the BQ field set to '.' so we cannot possibly satisfy this condition. The code will just accept the newly discovered evidence for alts at this site. 06 March 2014, 19:30:51 UTC
b5f5a9d apregier 06 March 2014, 18:17:26 UTC Merge branch 'my_annotation' into gb_master 06 March 2014, 18:17:26 UTC
646b6f2 apregier 06 March 2014, 18:15:13 UTC Restore Job::Iterator package 06 March 2014, 18:16:30 UTC
0d251f0 Jim Weible 06 March 2014, 16:20:47 UTC note the annoation-version param is deprecated 06 March 2014, 16:20:47 UTC
19db5d7 Jim Weible 06 March 2014, 16:20:25 UTC handle annotation data set correctly in the test 06 March 2014, 16:20:25 UTC
edce14c Jim Weible 28 February 2014, 15:57:28 UTC Revert "Revert "do the right thing with the copycat annotation"" This reverts commit e06fc4e36dd8092fee0b1f22eb730ce3a5a6ac8d. 06 March 2014, 14:03:59 UTC
5fe2924 Jim Weible 28 February 2014, 15:57:26 UTC Revert "Revert "write our temp files to a reasonable place"" This reverts commit 3cd0df3a9b7e6715ec16ea6cf02ef7706778bbbb. 06 March 2014, 14:03:58 UTC
a122cae Jim Weible 28 February 2014, 15:57:24 UTC Revert "Revert "fix up some copy pasta error messages"" This reverts commit 6055056b0dba9c93204e845b582a5f213384acdd. 06 March 2014, 14:03:58 UTC
8767185 Jim Weible 28 February 2014, 15:57:13 UTC Revert "Revert "create a dummy expected output file as standard for cnv detectors"" This reverts commit 5abef98c7ca3d5782240449500339ead9fc2b03e. 06 March 2014, 14:03:57 UTC
6cf65de APipe Tester 06 March 2014, 13:17:37 UTC Updated `gmt` tab completion. 06 March 2014, 13:17:37 UTC
1875d90 APipe Tester 06 March 2014, 13:16:49 UTC Updated `genome` tab completion. 06 March 2014, 13:16:49 UTC
76987f0 APipe Tester 06 March 2014, 13:15:12 UTC Updated class browser cache. 06 March 2014, 13:15:12 UTC
f99c881 apregier 06 March 2014, 02:32:45 UTC Merge branch 'my_annotation' into gb_master 06 March 2014, 02:32:45 UTC
1a02f30 apregier 06 March 2014, 02:31:01 UTC Don't break /gsc/bin/perl 06 March 2014, 02:31:01 UTC
430fa0e apregier 06 March 2014, 02:03:12 UTC Merge branch 'my_annotation' into gb_master 06 March 2014, 02:03:12 UTC
a738e51 apregier 05 March 2014, 22:58:54 UTC Check that builds weren't succeeded in between. 05 March 2014, 22:58:54 UTC
9a5d121 apregier 05 March 2014, 22:25:19 UTC Update cron 05 March 2014, 22:25:41 UTC
3816181 apregier 05 March 2014, 22:23:36 UTC Use exceptions 05 March 2014, 22:25:41 UTC
b096bb7 apregier 04 March 2014, 21:59:22 UTC Rewrite scan cron 05 March 2014, 22:25:40 UTC
b2b82c6 APipe Tester 05 March 2014, 22:22:16 UTC updated jenkins submodule to 8a9a322 05 March 2014, 22:22:16 UTC
609cb07 dmorton 05 March 2014, 20:51:17 UTC Stop trying to parse snv_detection_strategy for samtools info This was problematic for builds that had processing profiles that specified 'mpileup -BuDS' for instance since 'mpileup' is not a samtools pileup param. 05 March 2014, 20:53:09 UTC
ec22ef5 Chris Miller 05 March 2014, 20:24:32 UTC updated stderr message to make sense 05 March 2014, 20:24:32 UTC
0f66486 Chris Miller 05 March 2014, 20:02:47 UTC fixing hash reference bug 05 March 2014, 20:08:59 UTC
3d6b4fd Chris Miller 05 March 2014, 19:36:38 UTC adding reference-transcripts option to specify one that differs from the model 05 March 2014, 20:08:58 UTC
61bd7e1 Susanna Siebert 05 March 2014, 19:34:19 UTC need to use Test::More instead of Genome::Model::SomaticVariation::Command::TestHelpers 05 March 2014, 19:34:19 UTC
d90d1d7 Susanna Siebert 05 March 2014, 19:09:12 UTC fixed package name 05 March 2014, 19:22:40 UTC
f1ac2c9 Thomas Mooney 05 March 2014, 16:42:54 UTC Only examine the first 1000 lines of the BAM when discerning read length. Otherwise for large BAMs this process takes a *long* time without much gain in accuracy. 05 March 2014, 16:42:54 UTC
1ddec2d Susanna Siebert 05 March 2014, 15:12:02 UTC don't compare the output from reports/review.xml as that file will always be different 05 March 2014, 15:12:29 UTC
8ab9897 APipe Tester 05 March 2014, 14:00:26 UTC updated workflow submodule to 4332dce 05 March 2014, 14:00:26 UTC
2523308 Nathaniel Nutter 05 March 2014, 05:16:37 UTC pull up fetch utility 05 March 2014, 05:16:37 UTC
393784e Nathaniel Nutter 05 March 2014, 04:56:13 UTC refactor URL fetching Extracted similar code into a utility function and updated to use File::Fetch instead of shelling out to curl. 05 March 2014, 04:56:13 UTC
ca74757 Nathaniel Nutter 05 March 2014, 01:14:35 UTC delegate to local version if it is found If we update either of these normally people would't get them until they get deployed. With this delegation code in there it will try use the fact that someone is in a Git repo with the same executable to delegate to it. 05 March 2014, 01:15:47 UTC
5d93215 Nathaniel Nutter 04 March 2014, 21:41:57 UTC fixes RT #98012, shellcmd STDERR/STDOUT FCGI bug 05 March 2014, 00:49:37 UTC
0d56bbc Nathaniel Nutter 04 March 2014, 20:10:58 UTC can't use non-string variables in 3-argument open due to FCGI (I think) FCGI ties STDERR, STDOUT, and STDIN which overrides open calls. In the case of a 3-argument open it does: eval("$rc = open($_[0], $_[1], $_[2])"); Which means that the variables can't be "the normal 'reference to a glob'" as is supposed to be the case. 05 March 2014, 00:49:36 UTC
bbd8827 Nathaniel Nutter 04 March 2014, 20:08:01 UTC use parens 05 March 2014, 00:49:35 UTC
25785ae Nathaniel Nutter 04 March 2014, 20:06:28 UTC only backup STDOUT/STDERR if redirected 05 March 2014, 00:49:33 UTC
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