| 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 |
| 33f5b3b | Eddie Belter | 07 January 2013, 22:58:08 UTC | Sync: mv misc update library to library summary | 09 January 2013, 18:42:11 UTC |
| 6a204f5 | Eddie Belter | 07 January 2013, 22:57:17 UTC | Sync: misc updat subject test use_ok all subclasses | 09 January 2013, 18:42:10 UTC |
| fc7f341 | Eddie Belter | 07 January 2013, 22:55:25 UTC | Sync: misc update now subclasses based on subject class name | 09 January 2013, 18:42:10 UTC |
| 70fac8a | Eddie Belter | 07 January 2013, 22:29:57 UTC | Sync: rename misc update test | 09 January 2013, 18:42:10 UTC |
| c26dfa3 | Eddie Belter | 07 January 2013, 22:29:30 UTC | Sync: dir for misc updates | 09 January 2013, 18:42:09 UTC |
| a4a056e | Eddie Belter | 07 January 2013, 19:31:47 UTC | Sync: add lib summary to misc update reconciling | 09 January 2013, 18:42:09 UTC |
| 0c68530 | Eddie Belter | 07 January 2013, 19:31:16 UTC | Sync: add is UR::Object to lib summary | 09 January 2013, 18:42:09 UTC |
| d1738e2 | Eddie Belter | 03 January 2013, 23:10:54 UTC | Sync: Add library summary | 09 January 2013, 18:42:08 UTC |
| d1a7a21 | Eddie Belter | 03 January 2013, 23:02:57 UTC | Library: remove fragment_size_range, it is really called library_insert_size | 09 January 2013, 18:42:08 UTC |
| f5cb938 | Eddie Belter | 03 January 2013, 22:24:46 UTC | Library: rm protocol_name; add protocol, original and library insert size - all in table | 09 January 2013, 18:42:07 UTC |
| 7040c71 | Scott Smith | 09 January 2013, 18:37:24 UTC | updated test cases to produce more helpful debug output | 09 January 2013, 18:37:24 UTC |
| 5d77a26 | Scott Smith | 09 January 2013, 18:28:48 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 09 January 2013, 18:28:48 UTC |
| 43a2b43 | APipe Tester | 09 January 2013, 18:25:54 UTC | updated ur submodule to a10c039 | 09 January 2013, 18:25:54 UTC |
| f4b7767 | Malachi Griffith | 09 January 2013, 17:22:06 UTC | ClinSeq - update snv summary and convergence | 09 January 2013, 17:22:06 UTC |
| 0365a5f | Scott Smith | 09 January 2013, 16:08:54 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 09 January 2013, 16:08:54 UTC |
| b679cb5 | Scott Smith | 09 January 2013, 16:08:19 UTC | ensure Genome::Model::Define::BaseMinimal avoids adding an input to a define command when anything in its inheritance implements it (instead of just checking direct properties) | 09 January 2013, 16:08:19 UTC |
| a6ff6cd | apregier | 09 January 2013, 16:04:40 UTC | Merge branch 'fireteam2' into gb_master | 09 January 2013, 16:04:40 UTC |
| c77ab80 | Scott Smith | 09 January 2013, 16:02:51 UTC | update the log4perl observer to dump a call stack if it gets inappropriate parameters | 09 January 2013, 16:02:51 UTC |
| 204070c | Scott Smith | 09 January 2013, 16:02:18 UTC | complete replacement of hard-coded "/gsc/scripts/lib/java" with $ENV{GENOME_SW_LEGACY_JAVA} | 09 January 2013, 16:02:18 UTC |
| ced4aa2 | apregier | 08 January 2013, 23:38:02 UTC | Make diffs more specific | 09 January 2013, 16:01:36 UTC |
| c5d83c5 | Travis Abbott | 09 January 2013, 04:02:34 UTC | fix failing gmdefine gene-prediction tests recent changes made it so that the processing profile and model name were not passed along to the core bit of model definition code. this is an intermediate fix to make sure those attributes make their way to the right place. | 09 January 2013, 04:02:34 UTC |
| 1a946eb | Feiyu Du | 08 January 2013, 22:28:02 UTC | increase mem limit to 25g | 08 January 2013, 22:28:02 UTC |
| 7ae592c | Scott Smith | 08 January 2013, 21:44:54 UTC | updated convergence docs for latest synopsis generation | 08 January 2013, 21:44:54 UTC |
| d278dfc | Scott Smith | 08 January 2013, 21:40:32 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 08 January 2013, 21:40:32 UTC |
| 7d7744b | Nathan Nutter | 08 January 2013, 21:02:58 UTC | Revert "supress logging when self is not defined" This reverts commit cc1ec522adf9400618584666d014d5c71df0bf91. Upstream issue in UR is corrected, this observer should now receive the class name instead of undef. | 08 January 2013, 21:02:58 UTC |
| 04c90b4 | Scott Smith | 08 January 2013, 21:02:22 UTC | Updated synopsis definition results in new output for the define-docs test case. | 08 January 2013, 21:02:22 UTC |
| a052e8f | Scott Smith | 08 January 2013, 21:01:24 UTC | update test case to use --add-to-projects instead of --projects | 08 January 2013, 21:01:24 UTC |
| 397ec37 | Scott Smith | 08 January 2013, 21:00:22 UTC | Handle --add-to-projects correctly. Resolve the command name for the synopsis from command_name() instead of composing in manually, preventing an error on some models which override the processing profile subclass. | 08 January 2013, 21:00:22 UTC |
| 6d032be | Scott Smith | 08 January 2013, 20:58:20 UTC | if model create gets nothing at SUPER::create fail immediately instead of attempting to use an undefined $self | 08 January 2013, 20:58:20 UTC |
| 310d2a8 | Travis Abbott | 08 January 2013, 20:09:43 UTC | don't try to add processing_profile{,_id} to Define/Convergence | 08 January 2013, 20:09:43 UTC |
| d3b0755 | Eddie Belter | 08 January 2013, 19:47:26 UTC | Inst data import: add new basic importer w/ improved functionality | 08 January 2013, 19:47:26 UTC |
| df14db2 | Thomas Mooney | 08 January 2013, 16:30:01 UTC | Go for the target class directly when creating models. This fixes some old model definers that expect this behaviour (e.g. Somatic). | 08 January 2013, 16:30:01 UTC |
| 8bab1bb | apregier | 08 January 2013, 15:42:28 UTC | Merge branch 'fix' into gb_master | 08 January 2013, 15:42:28 UTC |
| 4fb6009 | apregier | 08 January 2013, 15:41:41 UTC | Update tests for new reference sequence import process | 08 January 2013, 15:42:04 UTC |
| 4312ce8 | Thomas Mooney | 08 January 2013, 15:17:40 UTC | Remove redundant processing-profile property. Quiets warnings. | 08 January 2013, 15:17:40 UTC |
| 448f61a | Thomas Mooney | 08 January 2013, 14:57:11 UTC | Remove tests of abstract parent class. Every concrete subclass has doc-generation tests, and the docs depend on the subclass, so these don't test a useful case. | 08 January 2013, 14:57:11 UTC |
| 3d06320 | Thomas Mooney | 08 January 2013, 14:56:17 UTC | Move the eval to the part that might fail. | 08 January 2013, 14:56:17 UTC |
| a0caf79 | Nathan Nutter | 08 January 2013, 02:50:41 UTC | diff was ~150 MB and causing email notification problems in Jenkins | 08 January 2013, 02:50:41 UTC |
| cc1ec52 | Nathan Nutter | 08 January 2013, 01:51:01 UTC | supress logging when self is not defined | 08 January 2013, 01:51:11 UTC |
| be64ca5 | Nathan Nutter | 08 January 2013, 01:49:35 UTC | update .test-tracker.conf | 08 January 2013, 01:51:11 UTC |
| 804093d | APipe Tester | 08 January 2013, 01:39:02 UTC | updated jenkins submodule to 55c6103 | 08 January 2013, 01:39:02 UTC |
| 775915f | APipe Tester | 08 January 2013, 01:37:17 UTC | updated jenkins submodule to 836bb89 | 08 January 2013, 01:37:17 UTC |
| 504b132 | APipe Tester | 07 January 2013, 23:37:58 UTC | updated ur submodule to b9a6490 | 07 January 2013, 23:37:58 UTC |
| abca3e8 | apregier | 07 January 2013, 21:22:21 UTC | Add strelka | 07 January 2013, 21:22:36 UTC |
| fe9d860 | Gabriel Sanderson | 07 January 2013, 21:20:02 UTC | Fixed a typo | 07 January 2013, 21:20:02 UTC |
| 4ed11d6 | Gabriel Sanderson | 07 January 2013, 21:16:31 UTC | Merge branch 'qchack' into gb_master | 07 January 2013, 21:16:31 UTC |
