| bb06c5c | Chris Miller | 24 January 2013, 01:48:37 UTC | Added submodule copyCat | 24 January 2013, 01:48:37 UTC |
| a7759bc | Nathan Nutter | 23 January 2013, 21:25:40 UTC | show doc IDs that were removed | 23 January 2013, 21:25:40 UTC |
| c820d2b | Nathan Nutter | 23 January 2013, 21:25:18 UTC | use status_message instead of print | 23 January 2013, 21:25:18 UTC |
| 12c8e93 | Nathan Nutter | 23 January 2013, 21:24:48 UTC | change status_message to debug_message | 23 January 2013, 21:24:48 UTC |
| 3e4ee6e | Nathan Nutter | 23 January 2013, 17:36:00 UTC | limit module_regex to .pm files | 23 January 2013, 17:36:14 UTC |
| d498d79 | Gabriel Sanderson | 22 January 2013, 22:46:12 UTC | Merge branch 'master' into gb_master | 22 January 2013, 22:46:12 UTC |
| c3d3a0c | Gabriel Sanderson | 22 January 2013, 22:45:53 UTC | Fixed the merged alignment result get so that multiple instrument data ids function. | 22 January 2013, 22:46:00 UTC |
| a8a9151 | Nathan Nutter | 22 January 2013, 21:58:37 UTC | check that directory paths are set Since $self->output_dir is not populated until $self->_prepare_output_directory is called someone could accidentally call _promote_data before that. | 22 January 2013, 21:59:46 UTC |
| db3fb38 | Nathan Nutter | 22 January 2013, 21:56:07 UTC | delete allocation(s) if aborting Trying to close some gaps in allocation handling for RT #89047. | 22 January 2013, 21:56:07 UTC |
| a899765 | Nathan Nutter | 22 January 2013, 21:54:52 UTC | delete allocation if aborting Trying to close some gaps in allocation handling for RT #89047. | 22 January 2013, 21:54:52 UTC |
| ac8ebf1 | Nathan Nutter | 22 January 2013, 21:52:55 UTC | setup staging dir within the eval Trying to close some gaps in allocation handling for RT #89047. | 22 January 2013, 21:52:55 UTC |
| 934f55f | Nathan Nutter | 22 January 2013, 21:42:42 UTC | Testing a theory about LSF state latency. | 22 January 2013, 21:42:59 UTC |
| c790fb7 | apregier | 22 January 2013, 20:18:17 UTC | Merge branch 'vep' into gb_master | 22 January 2013, 20:18:17 UTC |
| 98e65de | apregier | 22 January 2013, 20:07:27 UTC | First commit of new SV annotator This basically places the JWAnnot.pl script into a perl module, preparing for future development. | 22 January 2013, 20:08:20 UTC |
| 7d9b2fb | Malachi Griffith | 22 January 2013, 18:20:47 UTC | ClinSeq update to only warn about archived and set-do-not-archive status for last succeeded build | 22 January 2013, 18:20:47 UTC |
| 2d6c2cf | Chris Miller | 22 January 2013, 17:39:50 UTC | Added submodule cloneCaller | 22 January 2013, 17:39:50 UTC |
| 4758798 | Nathan Nutter | 22 January 2013, 16:01:58 UTC | switch a couple tests to use compare_ok | 22 January 2013, 16:02:56 UTC |
| d827867 | Nathan Nutter | 22 January 2013, 16:01:28 UTC | remove unused use | 22 January 2013, 16:02:55 UTC |
| 496bb56 | Nathan Nutter | 22 January 2013, 00:01:54 UTC | add global option to line filter | 22 January 2013, 16:02:55 UTC |
| dccbebd | Nathan Nutter | 21 January 2013, 08:03:10 UTC | refactor compare_ok's arg parsing It might be overly complex but the goal was to work like Test::More while also allowing additional options. Valid forms are: - file_1, file_2 - file_1, file_2, test_name - file_1, file_2, name => test_name, etc. - file_1, file_2, filters => qr(//) - file_1, file_2, filters => [qr(//), qr(//)] filters was previously just filter. | 22 January 2013, 16:02:54 UTC |
| 768310a | Nathan Nutter | 20 January 2013, 04:18:12 UTC | rename to compare_ok but keep diff_ok as alias for now | 22 January 2013, 16:02:54 UTC |
| 079328c | APipe Tester | 22 January 2013, 15:32:23 UTC | updated jenkins submodule to 64f4416 | 22 January 2013, 15:32:23 UTC |
| 8242817 | APipe Tester | 22 January 2013, 15:22:04 UTC | updated jenkins submodule to f7bb6e7 | 22 January 2013, 15:22:04 UTC |
| bc1020b | Scott Smith | 19 January 2013, 19:31:52 UTC | updated Genome::Model::Comparison examples, notes | 19 January 2013, 19:31:52 UTC |
| 90111fe | Scott Smith | 19 January 2013, 17:38:25 UTC | initial model comparison work w/ Jason | 19 January 2013, 17:38:25 UTC |
| 3d7240b | Scott Smith | 19 January 2013, 17:37:35 UTC | added comments around properties | 19 January 2013, 17:37:35 UTC |
| 595b72d | apregier | 18 January 2013, 22:32:27 UTC | Merge branch 'vep' into gb_master | 18 January 2013, 22:32:27 UTC |
| f35189e | apregier | 18 January 2013, 22:28:24 UTC | Fix bug in model define | 18 January 2013, 22:31:56 UTC |
| ef428d4 | Ian Ferguson | 18 January 2013, 21:52:18 UTC | Initial commit of Bwasw aligner module Initial commit of aligner module for Bwasw. Although Bwasw is a part of 'regular' Bwa, we decided to split it into its own module. The Bwasw module creates its reference index by finding the corresponding Bwa reference index, and creating symlinks to the index files (see PerLaneTophat.pm). This module contains its own SAM parser for fixing and modifying the SAM output from Bwasw. | 18 January 2013, 21:54:53 UTC |
| 146d57a | Gabriel Sanderson | 18 January 2013, 21:51:36 UTC | Merge branch 'simplify_vcf' into gb_master | 18 January 2013, 21:51:36 UTC |
| 1608ed9 | Gabriel Sanderson | 18 January 2013, 21:51:25 UTC | Added snv/indel vcf merging. Updated the test | 18 January 2013, 21:51:25 UTC |
| 100a582 | Gabriel Sanderson | 18 January 2013, 21:31:35 UTC | Merge branch 'simplify_vcf' into gb_master | 18 January 2013, 21:31:35 UTC |
| a5322ad | Gabriel Sanderson | 18 January 2013, 21:31:24 UTC | Updated the test to include indels. Fixed a typo. | 18 January 2013, 21:31:24 UTC |
| 85d0772 | Gabriel Sanderson | 18 January 2013, 21:24:13 UTC | Merge branch 'simplify_vcf' into gb_master | 18 January 2013, 21:24:13 UTC |
| ff80c51 | Gabriel Sanderson | 18 January 2013, 21:24:01 UTC | Some refactoring for including indels. Fixed test count. | 18 January 2013, 21:24:01 UTC |
| 06d8da9 | Gabriel Sanderson | 18 January 2013, 21:01:31 UTC | Merge branch 'simplify_vcf' into gb_master | 18 January 2013, 21:01:31 UTC |
| deb72b5 | Gabriel Sanderson | 18 January 2013, 20:59:00 UTC | Minor cleanup of SimplifyVcf and added a test. | 18 January 2013, 20:59:00 UTC |
| 1dc5c78 | APipe Tester | 18 January 2013, 20:19:49 UTC | updated jenkins submodule to 82c0d73 | 18 January 2013, 20:19:49 UTC |
| 695b3e5 | APipe Tester | 18 January 2013, 20:19:41 UTC | updated ur submodule to 45afcdd | 18 January 2013, 20:19:41 UTC |
| 0086701 | apregier | 18 January 2013, 19:57:58 UTC | Merge branch 'vep' into gb_master | 18 January 2013, 19:57:58 UTC |
| d502145 | apregier | 18 January 2013, 19:53:34 UTC | Get the blessed build from yaml file | 18 January 2013, 19:53:52 UTC |
| 05e79eb | Malachi Griffith | 18 January 2013, 19:23:12 UTC | clinseq: Added more ignore cases for diffing of clinseq test builds | 18 January 2013, 19:23:12 UTC |
| 873a129 | Gabriel Sanderson | 18 January 2013, 17:57:20 UTC | Merge branch 'master' into gb_master | 18 January 2013, 17:57:20 UTC |
| 8bfe2d9 | Gabriel Sanderson | 18 January 2013, 17:56:58 UTC | Corrected Data::Dumper::Dumper call | 18 January 2013, 17:56:58 UTC |
| ff96e3f | Malachi Griffith | 18 January 2013, 01:27:00 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 18 January 2013, 01:27:00 UTC |
| c6060db | Malachi Griffith | 18 January 2013, 01:26:39 UTC | Update tophat converge script to accomodate changes in rna-seq output | 18 January 2013, 01:26:39 UTC |
| 24c35eb | Charles Lu | 17 January 2013, 23:05:09 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 17 January 2013, 23:05:09 UTC |
| b87c9bb | Charles Lu | 17 January 2013, 23:05:03 UTC | Added the option to create a stacked bargraph in additon to dodge barplot | 17 January 2013, 23:05:03 UTC |
| e6c5090 | Nathan Nutter | 17 January 2013, 22:50:18 UTC | unset NO_LSF for this test | 17 January 2013, 23:00:19 UTC |
| e104c8c | Nathan Nutter | 17 January 2013, 21:45:53 UTC | add basic docs | 17 January 2013, 23:00:18 UTC |
| 0dead40 | Nathan Nutter | 17 January 2013, 21:25:12 UTC | fix diff test I didn't notice that the test earlier was text and not files. | 17 January 2013, 23:00:18 UTC |
| dc69c79 | Nathan Nutter | 17 January 2013, 21:21:04 UTC | remove "broken" tests compare returns 0 when there are no diffs so this was testing that the files were different; not the same. | 17 January 2013, 23:00:17 UTC |
| cca3e69 | Nathan Nutter | 17 January 2013, 21:14:02 UTC | add Genome::Utility::Test | 17 January 2013, 23:00:17 UTC |
| 39bcf37 | Nathan Nutter | 17 January 2013, 19:51:16 UTC | use compare for files, instead of compare_text | 17 January 2013, 23:00:16 UTC |
| 3a5999d | Nathan Nutter | 17 January 2013, 15:18:26 UTC | Reapply "No hardcoded path for $ENV{GENOME_TEST_URL}" | 17 January 2013, 23:00:16 UTC |
| f95e6db | Nathan Nutter | 17 January 2013, 17:17:38 UTC | alter tests to diff less aggressively There were several tests that broke when we changes the GENOME_TEST_TEMP directory path. A few were fixed already but these are a few more. In most cases this was improved by filtering out certain lines from output, e.g. paths and timestamps. | 17 January 2013, 23:00:16 UTC |
| 594d90a | Nathan Nutter | 17 January 2013, 19:09:01 UTC | whitespace | 17 January 2013, 23:00:15 UTC |
| d81545f | Nathan Nutter | 17 January 2013, 17:17:07 UTC | remove debug line | 17 January 2013, 23:00:15 UTC |
| 13a6f25 | Kyung Kim | 17 January 2013, 22:47:48 UTC | Send failed email when jobs fails | 17 January 2013, 22:47:48 UTC |
| a00e6bd | Malachi Griffith | 17 January 2013, 22:00:50 UTC | Merge branch 'master' of ssh://git/srv/git/genome Conflicts: lib/perl/Genome/Model/ClinSeq/Command/CreateMutationSpectrum.pm | 17 January 2013, 22:00:50 UTC |
| a4fa020 | Malachi Griffith | 17 January 2013, 21:57:35 UTC | Minor tweak to mutation spectrum | 17 January 2013, 21:57:35 UTC |
| d685a96 | Nathan Nutter | 17 January 2013, 16:55:41 UTC | add log message to help future troubleshooters | 17 January 2013, 17:09:17 UTC |
| 1a262f1 | Nathan Nutter | 17 January 2013, 16:53:13 UTC | make test more resilient - No longer diff the PNG files since they can differ for irrelevant reasons. - Improve the diff of the config file to remove a dependency on file paths. | 17 January 2013, 17:09:17 UTC |
| c85a669 | Thomas Mooney | 17 January 2013, 15:38:44 UTC | Add new releases for bowtie and tophat. | 17 January 2013, 15:38:44 UTC |
| af277ef | Nathan Nutter | 17 January 2013, 15:20:16 UTC | use /tmp instead of GENOME_TEST_TEMP Logic in Genome::Disk::Alllocation::_get_mount_path_from_full_path fails if the test's volume's mount_path is a subdirectory of another volume. | 17 January 2013, 15:22:18 UTC |
| b144de3 | Nathan Nutter | 17 January 2013, 15:17:53 UTC | Set NO_LSF so test's workflows run inline. | 17 January 2013, 15:17:53 UTC |
| 37207ac | Nathan Nutter | 17 January 2013, 15:15:01 UTC | Revert "No hardcoded path for $ENV{GENOME_TEST_URL}" This reverts commit 9888693365584cac823ecf3239b01210d8d7d731. | 17 January 2013, 15:15:01 UTC |
| 56655f8 | Dave Larson | 17 January 2013, 04:54:36 UTC | set GL exclusion as default | 17 January 2013, 04:54:36 UTC |
| b551f69 | Dave Larson | 17 January 2013, 04:46:32 UTC | removing deprecated mutation spectrum tool | 17 January 2013, 04:46:32 UTC |
| b934e2d | Dave Larson | 17 January 2013, 04:43:51 UTC | Drop use of gmt analysis mutation-spectrum | 17 January 2013, 04:44:05 UTC |
| 3252f0d | Dave Larson | 16 January 2013, 23:31:39 UTC | CHANGELOG Changes to SummarizeMutationSpectrum: * Excluding GL contigs is now an option and off by default. * Heterozygous variants where there is no reference allele are now included in the calculation. | 17 January 2013, 04:44:05 UTC |
| c062ab2 | Dave Larson | 16 January 2013, 22:23:43 UTC | change to all spaces | 17 January 2013, 04:44:04 UTC |
| dbc982e | Nathan Nutter | 17 January 2013, 02:51:36 UTC | add missing commas | 17 January 2013, 02:51:36 UTC |
| 67d9316 | Nathan Nutter | 16 January 2013, 19:17:56 UTC | fix for missing ROI | 17 January 2013, 02:50:23 UTC |
| 81417d7 | Scott Smith | 17 January 2013, 01:38:20 UTC | updated copy-number tools to use default files under genome/db | 17 January 2013, 01:38:20 UTC |
| d789f0c | Scott Smith | 17 January 2013, 01:37:50 UTC | updated pindel to use executable paths under /gsc/pkg/bio | 17 January 2013, 01:37:50 UTC |
| 956de7b | Scott Smith | 17 January 2013, 01:21:45 UTC | updated gmt copy-number cna-seg to use files in the tgi-misc-annotation file db | 17 January 2013, 01:21:51 UTC |
| f36bca7 | Ian Ferguson | 17 January 2013, 00:20:44 UTC | Fixed data loss issue when creating allocations Fixed an issue where data loss could occur when creating allocations. If the allocation system attempted to create an allocation that had an absolute path that already existed on the file system (and that path did not already have an allocation), that path would be deleted when the allocation system created and soon after deleted a "candidate" allocation for that path. Creating an allocation now checks for this condition. | 17 January 2013, 00:30:35 UTC |
| 9888693 | Ian Ferguson | 16 January 2013, 19:16:54 UTC | No hardcoded path for $ENV{GENOME_TEST_URL} Updated $ENV{GENOME_TEST_URL} in Site/TGI.pm so it no longer uses a hardcoded path. It now uses the directory specified by $ENV{GENOME_TEST_INPUTS}. | 17 January 2013, 00:30:34 UTC |
| e276c2d | Kyung Kim | 16 January 2013, 21:57:40 UTC | change file format .. earlier format was not formatted corrected for NCBI | 16 January 2013, 21:57:40 UTC |
| f06a90f | Feiyu Du | 16 January 2013, 21:40:47 UTC | Better handle TCGA sample names in vcf/base.pm | 16 January 2013, 21:40:47 UTC |
| 02a15ac | Travis Abbott | 16 January 2013, 20:55:57 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 16 January 2013, 20:55:57 UTC |
| 6664973 | Travis Abbott | 16 January 2013, 20:55:12 UTC | remove workflow include from MutationSpectrum.pm | 16 January 2013, 20:55:12 UTC |
| eb5b2e3 | Thomas Mooney | 16 January 2013, 20:36:21 UTC | Custom build diffing for GenePrediction::Bacterial. | 16 January 2013, 20:36:21 UTC |
| 4beee4c | Thomas Mooney | 16 January 2013, 16:44:28 UTC | Merge in new SV calls for validation. | 16 January 2013, 16:44:28 UTC |
| d7cba91 | apregier | 16 January 2013, 15:50:08 UTC | Merge branch 'fireteam2' into gb_master | 16 January 2013, 15:50:08 UTC |
| b9d17c4 | apregier | 16 January 2013, 00:28:10 UTC | Use gmt sam readcount instead of directly calling bam-readcount executable. | 16 January 2013, 15:49:32 UTC |
| b6f3019 | Malachi Griffith | 16 January 2013, 04:50:22 UTC | ClinSeq - added module to run various mutation-spectrum and mutation-rate analyses, associated tests | 16 January 2013, 04:50:22 UTC |
| 75c89d5 | Brian Derickson | 15 January 2013, 22:00:18 UTC | error messages should only be recorded to syslog if UR_DBI_NO_COMMIT is not set | 15 January 2013, 22:00:25 UTC |
| 4ba85ed | Jim Weible | 15 January 2013, 20:16:40 UTC | removed depricated stuff in dgidb hopkinsGroom | 15 January 2013, 20:16:40 UTC |
| d3810f4 | Jim Weible | 15 January 2013, 19:11:02 UTC | remove deprecated parts of Entrez dgidb importer | 15 January 2013, 19:11:09 UTC |
| ebac47a | Jim Weible | 15 January 2013, 18:48:23 UTC | remove deprecated parts of Ensembl importer | 15 January 2013, 19:11:09 UTC |
| 2d2a8f4 | apregier | 15 January 2013, 18:51:22 UTC | Merge branch 'fireteam2' into gb_master | 15 January 2013, 18:51:22 UTC |
| 8eacccd | apregier | 15 January 2013, 18:50:44 UTC | Fix package name | 15 January 2013, 18:51:15 UTC |
| 5dc4ba6 | APipe Tester | 15 January 2013, 18:34:30 UTC | updated jenkins submodule to 9896827 | 15 January 2013, 18:34:30 UTC |
| 43efbe0 | Gabriel Sanderson | 15 January 2013, 18:18:13 UTC | Merge branch 'vcf_version' into gb_master | 15 January 2013, 18:18:13 UTC |
| a412c48 | Gabriel Sanderson | 15 January 2013, 18:17:55 UTC | Increase vcf_version so we produce combined vcf indel files and tcga indel files. | 15 January 2013, 18:18:02 UTC |
| 60e12cf | APipe Tester | 15 January 2013, 18:00:46 UTC | updated jenkins submodule to a44c5c4 | 15 January 2013, 18:00:46 UTC |
| 4a9f47c | apregier | 15 January 2013, 17:50:51 UTC | Merge branch 'fireteam2' into gb_master | 15 January 2013, 17:50:51 UTC |
| 4e62d7d | apregier | 14 January 2013, 20:04:18 UTC | New strelka location and new strelka version | 15 January 2013, 17:50:33 UTC |
