| 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 |
| 65eb1d9 | Jim Weible | 15 January 2013, 16:57:04 UTC | remove deprecated piece from dgene importer | 15 January 2013, 16:57:04 UTC |
| 89f153b | Jim Weible | 15 January 2013, 16:21:44 UTC | remove entity creation from drugbank importer as it is deprecated #DONT_DO_IT | 15 January 2013, 16:21:44 UTC |
| 2eb672f | Scott Smith | 15 January 2013, 01:15:29 UTC | add file names to error messages | 15 January 2013, 01:15:29 UTC |
| b965c78 | Gabriel Sanderson | 14 January 2013, 20:52:59 UTC | Merge branch 'tcga' into gb_master | 14 January 2013, 20:52:59 UTC |
| a908f0b | Gabriel Sanderson | 14 January 2013, 20:37:43 UTC | Handle things appropriately if no vcfProcessLog lines exist. Updated test. | 14 January 2013, 20:52:50 UTC |
| 6995de4 | Malachi Griffith | 14 January 2013, 20:46:42 UTC | Clinseq - various updates to converge scripts | 14 January 2013, 20:46:42 UTC |
| 3c037cb | APipe Tester | 14 January 2013, 19:42:30 UTC | updated jenkins submodule to 4a7aa33 | 14 January 2013, 19:42:30 UTC |
| ad3ab1a | APipe Tester | 14 January 2013, 19:38:31 UTC | updated jenkins submodule to e0fad0e | 14 January 2013, 19:38:31 UTC |
| 51fff8b | APipe Tester | 14 January 2013, 19:01:37 UTC | updated jenkins submodule to 27e1863 | 14 January 2013, 19:01:37 UTC |
| 90e99fc | APipe Tester | 14 January 2013, 19:01:24 UTC | updated ur submodule to f97aea9 | 14 January 2013, 19:01:24 UTC |
| c36c538 | Nathan Nutter | 14 January 2013, 15:49:04 UTC | add comment | 14 January 2013, 15:49:04 UTC |
| 52e2099 | Nathan Nutter | 14 January 2013, 15:29:50 UTC | emit more explicit error messages | 14 January 2013, 15:41:55 UTC |
| c9cd3d6 | Scott Smith | 14 January 2013, 15:19:59 UTC | added GENOME_FS_LOCAL_NETWORK_CACHE environment variable to replace hard-coded /var/cache/tgisan and updated Genome::Site::TGI | 14 January 2013, 15:19:59 UTC |
| 27cf97c | Scott Smith | 14 January 2013, 13:31:58 UTC | Genome::Model::ClinSeq now inherits directly from Genome::Model instead of Genome::ModelDeprecated | 14 January 2013, 13:31:58 UTC |
| c0c5361 | Scott Smith | 14 January 2013, 13:27:35 UTC | cleanup Genome::Model The updated Genome::Model class now has doc lines for everything. The subject_class_name property is now an indirect accessor instead of r/w. The column in the db (non-nullable) is now bound to _subject_class_name until all old snapshots are removed, and it can be dropped. Properties which are deprecated but still needed by things which are not using ModelDeprecated as a base class (tweeners) are in their own section. Pipelines such as ClinSeq can now abandon ModelDeprecated completely, and hopefully somatic variation will follow soon. Notes are present throughout the module as to the status of legacy parts. | 14 January 2013, 13:27:35 UTC |
| 8a031ad | Scott Smith | 14 January 2013, 05:27:09 UTC | updated to not do deep copy, but not share references either | 14 January 2013, 05:27:09 UTC |
| 133e382 | Scott Smith | 13 January 2013, 23:28:14 UTC | actually remove compare_pp_and_model_type from model define command BaseMinimal | 13 January 2013, 23:28:14 UTC |
| 764adc1 | Scott Smith | 13 January 2013, 23:15:52 UTC | Cleanup of Genome::Model::Command::Define::BaseMinimal The way that this class copied model property data led to shared references, and too many attributes being passed through. This is now fixed. In addition, the base definer now lets the model validate its own processing profile and inputs instead of doing it in the command. The _validate_inputs, validate_processing_profile, and compare_pp_and_model_type methods are now removed from this class and also the old ::Helper subclass from which it was pulled-up. | 13 January 2013, 23:15:52 UTC |
| 9a3ac1f | Scott Smith | 13 January 2013, 23:15:28 UTC | ensure that when model subclasses are extended dynamically that the processing_profile property has a doc field, as it will transfer to the define command | 13 January 2013, 23:15:28 UTC |
| 6cb1dce | APipe Tester | 12 January 2013, 06:26:36 UTC | updated jenkins submodule to 00dc37d | 12 January 2013, 06:26:36 UTC |
| 25c82b5 | Gabriel Sanderson | 12 January 2013, 00:15:31 UTC | Merge branch 'validation' into gb_master | 12 January 2013, 00:15:31 UTC |
| c96489e | Gabriel Sanderson | 12 January 2013, 00:15:18 UTC | CHANGELOG: In SomaticValidation builds, all validation related files are now in the validation/ directory. | 12 January 2013, 00:15:27 UTC |
| c61cd60 | Scott Smith | 11 January 2013, 23:21:25 UTC | use $ENV{GENOME_SW} to run GATK | 11 January 2013, 23:21:25 UTC |
| 6409381 | Charles Lu | 11 January 2013, 21:36:05 UTC | fixed a bug so it will differentiate between 2 samples with same name but different type (AML001_tumor vs AML001_relapse) | 11 January 2013, 21:36:05 UTC |
| bc7f4dd | Gabriel Sanderson | 11 January 2013, 21:22:18 UTC | Merge branch 'backfill' into gb_master | 11 January 2013, 21:22:18 UTC |
| 19fc6e0 | Gabriel Sanderson | 08 January 2013, 22:23:23 UTC | CHANGELOG: Fixed create-cross-sample-vcf. Assume BQ and AD values from reference on incoming vcf lines. | 11 January 2013, 21:22:15 UTC |
| 020a291 | Nathan Nutter | 11 January 2013, 21:20:38 UTC | subtest is not in our Test::More | 11 January 2013, 21:20:38 UTC |
| cf9903f | Nathan Nutter | 11 January 2013, 20:25:41 UTC | update test to catch read-only filesystem failure | 11 January 2013, 20:25:41 UTC |
| eee5446 | Nathan Nutter | 11 January 2013, 20:12:08 UTC | refactor test using subtests | 11 January 2013, 20:12:08 UTC |
| fad4333 | Nathan Nutter | 11 January 2013, 19:30:17 UTC | remove comment | 11 January 2013, 19:30:17 UTC |
| d8ba8e0 | Nathan Nutter | 11 January 2013, 19:29:32 UTC | get date template from UR::Context | 11 January 2013, 19:29:32 UTC |
| 5f9df7a | Nathan Nutter | 11 January 2013, 19:05:16 UTC | make sure example_build is newer than build so it is used by commands when build is not specified | 11 January 2013, 19:24:55 UTC |
| 5880792 | APipe Tester | 11 January 2013, 19:22:44 UTC | updated ur submodule to fbfa32b | 11 January 2013, 19:22:44 UTC |
| 7ab97e4 | APipe Tester | 11 January 2013, 19:09:59 UTC | updated ur submodule to 04b47ec | 11 January 2013, 19:09:59 UTC |
| 880af7f | Anthony Brummett | 11 January 2013, 14:31:33 UTC | Make it work when run multiple times in the same process Copy the hash of formats to a function-local var before deleting it's keys | 11 January 2013, 14:31:33 UTC |
| b3913e5 | Scott Smith | 11 January 2013, 12:04:37 UTC | replaced hard-coded path to /gsc/bin/bam-check with $ENV{GENOME_SW} based path, and skipped the shell wrapper and symlink to prevent silent changing of versions | 11 January 2013, 12:04:37 UTC |
| 73d4b6b | Thomas Mooney | 10 January 2013, 23:53:00 UTC | Try to reallocate at the end of the import process. | 10 January 2013, 23:53:54 UTC |
| 27189d7 | Nathan Nutter | 10 January 2013, 22:46:49 UTC | scheduled != completed | 10 January 2013, 23:51:34 UTC |
| 934bd76 | Nathan Nutter | 10 January 2013, 22:47:26 UTC | set date_completed explicitly | 10 January 2013, 23:51:33 UTC |
| b4c2212 | Nathan Nutter | 10 January 2013, 23:50:58 UTC | ensure timestamps are staggered | 10 January 2013, 23:51:14 UTC |
| 20c139d | Gabriel Sanderson | 10 January 2013, 20:51:46 UTC | Adjust files ignored by diff for the new tcga indels files. | 10 January 2013, 20:51:46 UTC |
| 22eebe3 | Anthony Brummett | 10 January 2013, 18:58:15 UTC | Avoid a warning about calling defined() on a list | 10 January 2013, 18:58:15 UTC |
| 4a23a95 | Nathan Nutter | 10 January 2013, 17:18:19 UTC | skip . and .. dirs instead of expecting readdir to be sorted The . and .. dirs did not come first on some hosts so this changes them to be skipped as the parent directory is read instead of having to assume they come first. | 10 January 2013, 17:18:19 UTC |
| cdc2210 | Nathan Nutter | 10 January 2013, 02:44:25 UTC | do not copy UR::Objects | 10 January 2013, 02:44:25 UTC |
| 87846e3 | Nathan Nutter | 09 January 2013, 22:34:56 UTC | remove unknown property: large_indel_output_bed | 09 January 2013, 23:42:06 UTC |
| a2d558b | Nathan Nutter | 09 January 2013, 22:32:39 UTC | override max_memory with custom accessor Workflow does not yet support dynamically changing lsf_resource so we have to throttle max_memory based on the LSF environment. We would probably also want to do this based on available memory if outside LSF. Set default LSF memory to 16 GB based on previously hard-coded value in Genome::Model::SomaticValidation::Command::ValidateSmallIndels. Had to change max_memory format to be explicity in GB. | 09 January 2013, 23:42:05 UTC |
| 627769a | Nathan Nutter | 09 January 2013, 22:13:07 UTC | make kilobytes_requested test fuzzy kilobytes_requested is estimated based on an expected compression and may vary depending on the version of the compression library. | 09 January 2013, 22:13:07 UTC |
| b4bc037 | APipe Tester | 09 January 2013, 21:49:27 UTC | updated ur submodule to c0cdbae | 09 January 2013, 21:49:27 UTC |
| 1eed5dd | Gabriel Sanderson | 09 January 2013, 19:58:18 UTC | Merge branch 'indelvcf' into gb_master | 09 January 2013, 19:58:18 UTC |
| de25ff6 | Gabriel Sanderson | 08 January 2013, 23:54:30 UTC | CHANGELOG: Generate indel vcfs in combine operations. Create an indel TCGA file in somatic variation. | 09 January 2013, 19:40:18 UTC |
| 92cdcb8 | Eddie Belter | 09 January 2013, 18:55:13 UTC | Build Unarchive: set data directory ot disk alloc abs path | 09 January 2013, 18:55:13 UTC |
| 8a19e8b | Eddie Belter | 09 January 2013, 18:41:53 UTC | Sync: print status when executing pidfa sql; capture genotype file update in eval | 09 January 2013, 18:42:14 UTC |
| b286972 | Eddie Belter | 09 January 2013, 18:41:09 UTC | Microarray: check disk alloc absolute path when copying file | 09 January 2013, 18:42:14 UTC |
| 9467137 | Eddie Belter | 08 January 2013, 23:08:41 UTC | Library: add new properties to test | 09 January 2013, 18:42:14 UTC |
| ee0fa77 | Eddie Belter | 08 January 2013, 00:37:13 UTC | Sync: change var names in reconcile misc update | 09 January 2013, 18:42:13 UTC |
| 9a436bb | Eddie Belter | 08 January 2013, 00:36:19 UTC | Sync: update subject tests to accomodatre unsupported class | 09 January 2013, 18:42:13 UTC |
| 14e78fe | Eddie Belter | 08 January 2013, 00:11:39 UTC | Sync: add perform_update method to pg mem and sample attr | 09 January 2013, 18:42:13 UTC |
| a0a132d | Eddie Belter | 07 January 2013, 23:54:17 UTC | Sync: added unsupported class to handle unknown misc updates | 09 January 2013, 18:42:12 UTC |
| 160f183 | Eddie Belter | 07 January 2013, 23:34:54 UTC | Sync: add sample attr and pop group member misc update subclasses | 09 January 2013, 18:42:12 UTC |
| edf8fdf | Eddie Belter | 07 January 2013, 23:34:26 UTC | Sync: move multi misc update to dir; update class names | 09 January 2013, 18:42:12 UTC |
| 5331bae | Eddie Belter | 07 January 2013, 23:12:35 UTC | Sync: lib summary perform update does update | 09 January 2013, 18:42:11 UTC |
