| 7306613 | Thomas B. Mooney | 07 April 2015, 13:28:00 UTC | Merge pull request #638 from tmooney/spaces_in_picard_arguments Allow spaces in comments again. | 07 April 2015, 13:28:00 UTC |
| d552b4e | Thomas Mooney | 07 April 2015, 13:03:42 UTC | Allow spaces in comments again. This commit was produced in Saint Louis, Missouri, USA. | 07 April 2015, 13:03:42 UTC |
| f905399 | APipe Tester | 06 April 2015, 18:49:43 UTC | updated jenkins submodule to 08335ed | 06 April 2015, 19:59:01 UTC |
| 0730304 | Susanna Siebert | 06 April 2015, 19:37:43 UTC | Merge pull request #627 from susannasiebert/variant_reporting_vep Change ON_TARGET merge strategy to uniq-concat | 06 April 2015, 19:37:43 UTC |
| 9342665 | Thomas B. Mooney | 06 April 2015, 19:29:18 UTC | Merge pull request #620 from tmooney/deduplicate_picard_histogram Deduplicate histogram and metrics processing subroutines. | 06 April 2015, 19:29:18 UTC |
| fa44ef7 | Thomas B. Mooney | 06 April 2015, 19:28:38 UTC | Merge pull request #615 from tmooney/remove_check_for_errors_without_eval Remove useless use of $@ not with eval... | 06 April 2015, 19:28:38 UTC |
| 76bb598 | Dave Larson | 06 April 2015, 17:22:38 UTC | Merge pull request #633 from tmooney/build_requested_cleverness Fix BQM's ability to decide what column to use for "build_requested". | 06 April 2015, 17:22:38 UTC |
| 44775d5 | Thomas B. Mooney | 06 April 2015, 15:32:25 UTC | Merge pull request #614 from tmooney/pass_the_vcf_sample_name_to_picard Picard needs to know the name in the VCF. | 06 April 2015, 15:32:25 UTC |
| 58dad41 | Thomas Mooney | 06 April 2015, 15:08:32 UTC | Fix broken indirection. | 06 April 2015, 15:08:32 UTC |
| c911f7f | Nathaniel Nutter | 06 April 2015, 14:51:44 UTC | Merge pull request #625 from nnutter/tgisan migrate off of `tgisan` and `unknown` scopes | 06 April 2015, 14:51:44 UTC |
| cf16851 | Nathaniel Nutter | 06 April 2015, 14:49:28 UTC | Merge pull request #632 from nnutter/master fix typo during LockProxy conversion | 06 April 2015, 14:49:28 UTC |
| 2abfdfc | Nathaniel Nutter | 04 April 2015, 19:15:29 UTC | fix typo during LockProxy conversion | 04 April 2015, 19:15:29 UTC |
| ee32b2e | APipe Tester | 04 April 2015, 12:17:46 UTC | Updated `gmt` tab completion. | 04 April 2015, 12:17:46 UTC |
| 2d46aa1 | APipe Tester | 04 April 2015, 12:16:54 UTC | Updated `genome` tab completion. | 04 April 2015, 12:16:54 UTC |
| dd24fa0 | Eddie Belter | 03 April 2015, 23:11:34 UTC | Merge pull request #631 from ebelter/sync Sync: fix lock parameter | 03 April 2015, 23:11:34 UTC |
| b1714d7 | Eddie Belter | 03 April 2015, 22:56:23 UTC | Sync: fix lock parameter | 03 April 2015, 22:56:23 UTC |
| 647c068 | Nathaniel Nutter | 03 April 2015, 04:46:26 UTC | start migration off of `unknown` scope | 03 April 2015, 21:19:52 UTC |
| ddb9be4 | Nathaniel Nutter | 03 April 2015, 00:42:33 UTC | start migration off of `tgisan` | 03 April 2015, 21:19:51 UTC |
| 9f0daa4 | Nathaniel Nutter | 02 April 2015, 22:18:01 UTC | add `host` scope for locking | 03 April 2015, 21:19:50 UTC |
| 705205b | Nathaniel Nutter | 02 April 2015, 21:59:21 UTC | add "namespace" support for NessyBackend | 03 April 2015, 21:19:50 UTC |
| b83be9d | Nathaniel Nutter | 03 April 2015, 21:18:43 UTC | Merge pull request #624 from nnutter/genome-env break circular dependency between Genome, Genome::Env, and Genome::Site::TGI | 03 April 2015, 21:18:43 UTC |
| d4d365e | Nathaniel Nutter | 03 April 2015, 21:18:23 UTC | Merge pull request #626 from nnutter/lock_resource minimize use of Genome::Sys::Lock API | 03 April 2015, 21:18:23 UTC |
| 910ffe0 | Nathaniel Nutter | 03 April 2015, 21:17:48 UTC | Merge pull request #619 from nnutter/RT-104979 only build workflows should go in build workflow queue | 03 April 2015, 21:17:48 UTC |
| 70c644c | Nathaniel Nutter | 03 April 2015, 17:23:05 UTC | convert genome-webserver scripts to LockProxy | 03 April 2015, 19:22:07 UTC |
| be97dae | Nathaniel Nutter | 03 April 2015, 17:18:04 UTC | remove legacy locking methods | 03 April 2015, 19:22:06 UTC |
| 8c63895 | Nathaniel Nutter | 03 April 2015, 17:15:24 UTC | use LockProxy in LockMigrationProxy.t | 03 April 2015, 19:22:04 UTC |
| 79397a2 | Avinash Ramu | 03 April 2015, 19:18:03 UTC | Merge pull request #621 from gatoravi/clinseq_bedtools_path Figure out bedtools path better | 03 April 2015, 19:18:03 UTC |
| 8064564 | Eddie Belter | 03 April 2015, 18:57:44 UTC | Merge pull request #612 from ebelter/cghub-metadata-create-from-xml GMT CG Hub: metadata can be created from XML and file | 03 April 2015, 18:57:44 UTC |
| 9e9ad10 | Eddie Belter | 03 April 2015, 18:57:37 UTC | Merge pull request #616 from ebelter/cghub-query-with-rest-api CG Hub: query uses rest API | 03 April 2015, 18:57:37 UTC |
| bd10318 | Susanna Siebert | 03 April 2015, 17:28:52 UTC | change ON_TARGET merge strategy to uniq-concat | 03 April 2015, 17:28:52 UTC |
| a193dc5 | Avinash Ramu | 03 April 2015, 16:33:07 UTC | Don't duplicate | 03 April 2015, 16:33:07 UTC |
| deeee90 | Nathaniel Nutter | 03 April 2015, 05:00:31 UTC | restore Process to run in workflow queue | 03 April 2015, 05:00:31 UTC |
| 64cd99e | Nathaniel Nutter | 02 April 2015, 22:44:13 UTC | load Env modules before Site (break circular dependencies) Some things in Site depend on default values from Genome::Env. | 03 April 2015, 00:37:33 UTC |
| bc8bf68 | Nathaniel Nutter | 02 April 2015, 22:43:45 UTC | move default value to env module | 03 April 2015, 00:37:31 UTC |
| 6cef3a4 | Nathaniel Nutter | 02 April 2015, 22:42:51 UTC | break circular dependencies Genome required Genome::Env so Genome::Env shouldn't require Genome. | 03 April 2015, 00:37:12 UTC |
| 6004230 | APipe Tester | 02 April 2015, 22:42:36 UTC | updated ur submodule to af01a9f | 02 April 2015, 22:42:36 UTC |
| 8590c72 | Thomas Mooney | 02 April 2015, 21:21:31 UTC | Test for definedness rather than truthiness. | 02 April 2015, 21:21:31 UTC |
| 0f59624 | Avinash Ramu | 02 April 2015, 20:45:47 UTC | figure out bedtools path better | 02 April 2015, 20:45:47 UTC |
| d95ff0c | Eddie Belter | 02 April 2015, 20:39:18 UTC | Merge pull request #609 from ebelter/instdata-generate-cmds InstData Generate Cmds: check if file is empty | 02 April 2015, 20:39:18 UTC |
| 668075e | Eddie Belter | 02 April 2015, 19:52:37 UTC | CG Hub: rename create to create_from_xml to avoid storing xml and parsed data structure | 02 April 2015, 19:52:37 UTC |
| 284d2b9 | Thomas Mooney | 02 April 2015, 19:42:53 UTC | Deduplicate histogram and metrics processing subroutines. | 02 April 2015, 19:42:53 UTC |
| 0585447 | Thomas B. Mooney | 02 April 2015, 19:01:52 UTC | Merge pull request #610 from tmooney/remove_unused_sr_vars_in_identifydnp Remove disused variables. | 02 April 2015, 19:01:52 UTC |
| 69b6f64 | Dave Larson | 02 April 2015, 18:11:16 UTC | Merge pull request #618 from ernfrid/add_readcount_checks Add readcount checks | 02 April 2015, 18:11:16 UTC |
| 59a4367 | Nathaniel Nutter | 02 April 2015, 16:16:15 UTC | change other queues similar to issue with RT#104979 | 02 April 2015, 16:16:15 UTC |
| 5f1ace0 | Nathaniel Nutter | 02 April 2015, 16:14:18 UTC | change queue as requested in RT#104979 | 02 April 2015, 16:14:18 UTC |
| 5ad22c3 | Susanna Siebert | 02 April 2015, 14:09:48 UTC | Merge pull request #589 from susannasiebert/process_tests2 Framework for process tests | 02 April 2015, 14:09:48 UTC |
| d829a74 | Thomas B. Mooney | 02 April 2015, 13:54:48 UTC | Merge pull request #599 from tmooney/prefer_an_original_reference_in_fl_merge Narrow down choices of convertible references by preferring an input. | 02 April 2015, 13:54:48 UTC |
| 2c750d7 | Thomas B. Mooney | 02 April 2015, 13:08:04 UTC | Merge pull request #611 from tmooney/restore_the_not_really_disused_method Revert "Remove incomplete disused "parse_file_into_histogram_hashref"." | 02 April 2015, 13:08:04 UTC |
| 9e5a776 | APipe Tester | 02 April 2015, 12:18:24 UTC | Updated `gmt` tab completion. | 02 April 2015, 12:18:24 UTC |
| c8944a0 | APipe Tester | 02 April 2015, 12:17:32 UTC | Updated `genome` tab completion. | 02 April 2015, 12:17:32 UTC |
| 01eb83f | APipe Tester | 02 April 2015, 12:15:27 UTC | Updated class browser cache. | 02 April 2015, 12:15:27 UTC |
| 8b648ed | Dave Larson | 02 April 2015, 03:23:32 UTC | update docs slightly | 02 April 2015, 03:23:32 UTC |
| 7d479e7 | Dave Larson | 02 April 2015, 03:07:18 UTC | add some checking to ensure filtering doesn't occur when hitting multiple BAMs | 02 April 2015, 03:07:18 UTC |
| 2a1d728 | Nathaniel Nutter | 01 April 2015, 23:20:37 UTC | Merge pull request #592 from nnutter/lock-pair LockProxy and LockMigrationProxy | 01 April 2015, 23:20:37 UTC |
| 91c63f3 | Eddie Belter | 01 April 2015, 22:26:04 UTC | CG Hub: query uses rest API | 01 April 2015, 22:26:04 UTC |
| 48010bd | Thomas Mooney | 01 April 2015, 22:15:33 UTC | Remove useless use of $@ not with eval... ...and the unused $err variable that comes with it! | 01 April 2015, 22:15:33 UTC |
| 982978d | Eddie Belter | 01 April 2015, 21:39:55 UTC | CG Hub: query uses full query, not just uuid | 01 April 2015, 21:39:55 UTC |
| 59e9f6f | Thomas Mooney | 01 April 2015, 21:36:00 UTC | Picard needs to know the name in the VCF. (This is different from the name for TCGA samples, for example.) | 01 April 2015, 21:36:00 UTC |
| 2141b63 | Eddie Belter | 01 April 2015, 21:14:55 UTC | GMT CG Hub: metadata can be created from XML and file | 01 April 2015, 21:14:55 UTC |
| 166fc83 | Thomas B. Mooney | 01 April 2015, 20:41:01 UTC | Merge pull request #608 from tmooney/make_available_the_new_fl_on_merge Make new_feature_list output available from merge. | 01 April 2015, 20:41:01 UTC |
| 64be6ee | Thomas Mooney | 01 April 2015, 20:20:11 UTC | Revert "Remove incomplete disused "parse_file_into_histogram_hashref"." This reverts commit fdbcd444d7ea17d24014c8d6af86525b749d6eae. | 01 April 2015, 20:20:11 UTC |
| 3881edc | Nathaniel Nutter | 01 April 2015, 19:06:27 UTC | validate that `new()` is called as a class method | 01 April 2015, 19:06:27 UTC |
| d97a6aa | Nathaniel Nutter | 01 April 2015, 18:57:25 UTC | break apart LOCK_RESOURCE_PARAMS_SPEC for better reuse | 01 April 2015, 18:57:25 UTC |
| 2fa7607 | Nathaniel Nutter | 01 April 2015, 18:48:05 UTC | deduplicate use of `random_string` and improve impl. performance | 01 April 2015, 18:48:05 UTC |
| 64d71e3 | Thomas Mooney | 01 April 2015, 18:18:58 UTC | Use UR::Util::intersect_lists instead of rolling our own intersection. | 01 April 2015, 18:18:58 UTC |
| 4a6ffb7 | Susanna Siebert | 01 April 2015, 18:06:23 UTC | Merge pull request #582 from susannasiebert/qc_framework Create qc tool wrappers | 01 April 2015, 18:06:23 UTC |
| 87e82e1 | Thomas Mooney | 01 April 2015, 17:56:21 UTC | Remove disused variables. Not only are they not used, they duplicate two other variables declared just above them! | 01 April 2015, 17:56:21 UTC |
| 5409982 | Eddie Belter | 01 April 2015, 16:50:39 UTC | InstData Generate Cmds: rm headers check | 01 April 2015, 16:50:39 UTC |
| 215f09b | Thomas B. Mooney | 01 April 2015, 15:54:54 UTC | Merge pull request #606 from tmooney/gmt_picard_typos Fix gmt picard typos; remove duplicate method | 01 April 2015, 15:54:54 UTC |
| db39485 | Thomas B. Mooney | 01 April 2015, 15:49:13 UTC | Merge pull request #583 from tmooney/AT-750-v3 Add decorators and a "QC" decorator to the Alignment Dispatcher | 01 April 2015, 15:49:13 UTC |
| 00250a7 | Thomas B. Mooney | 01 April 2015, 15:48:21 UTC | Merge pull request #578 from tmooney/deduplicate_alignment_queue_selection Stop using GENOME_LSF_QUEUE_ALIGNMENT_PROD. | 01 April 2015, 15:48:21 UTC |
| 9393f43 | Susanna Siebert | 01 April 2015, 15:13:46 UTC | Merge pull request #605 from susannasiebert/model_tests Fix class name | 01 April 2015, 15:13:46 UTC |
| bcf7670 | Eddie Belter | 01 April 2015, 00:02:20 UTC | InstData Generate Cmds: check if file is empty | 01 April 2015, 00:02:20 UTC |
| 9889816 | Nathaniel Nutter | 31 March 2015, 20:50:35 UTC | remove unused function | 31 March 2015, 20:50:35 UTC |
| 27e569e | Thomas Mooney | 31 March 2015, 19:46:31 UTC | Make new_feature_list output available from merge. This makes merge more similar to import, both of which are being used in by LIMS for similar purposes. | 31 March 2015, 19:46:31 UTC |
| c628a80 | Dave Larson | 31 March 2015, 18:48:05 UTC | Merge pull request #603 from ernfrid/bump_bam_readcount change default version of G::M::T::Sam::Readcount to use bam-readcount v... | 31 March 2015, 18:48:05 UTC |
| 67d7d9b | Thomas B. Mooney | 31 March 2015, 18:06:00 UTC | Merge pull request #597 from tmooney/call_correct_accessor_in_adsp_qc Call Correct Accessor in ADSP QC tools | 31 March 2015, 18:06:00 UTC |
| aba1942 | Nathaniel Nutter | 31 March 2015, 16:16:51 UTC | Merge pull request #604 from nnutter/RT-104865 avoid crash when chromosome is missing | 31 March 2015, 16:16:51 UTC |
| 3f31962 | Nathaniel Nutter | 31 March 2015, 16:16:46 UTC | Merge pull request #600 from nnutter/RT-104836 handle use case where reference sequence is missing | 31 March 2015, 16:16:46 UTC |
| fdbcd44 | Thomas Mooney | 31 March 2015, 15:55:12 UTC | Remove incomplete disused "parse_file_into_histogram_hashref". | 31 March 2015, 15:55:12 UTC |
| ec2d651 | Susanna Siebert | 31 March 2015, 15:34:26 UTC | Merge remote-tracking branch 'origin/master' into qc_framework | 31 March 2015, 15:34:26 UTC |
| 2574ab4 | Thomas Mooney | 31 March 2015, 15:23:37 UTC | Check for the method we're really going to call. | 31 March 2015, 15:23:37 UTC |
| 6c8ad8f | Thomas Mooney | 31 March 2015, 15:23:00 UTC | Fix typo: hashsref => hashref | 31 March 2015, 15:23:00 UTC |
| ac0714c | Susanna Siebert | 31 March 2015, 15:16:27 UTC | Explicitly test that there is only one metric_key in the metric_results | 31 March 2015, 15:16:27 UTC |
| 0063af8 | Susanna Siebert | 31 March 2015, 14:55:27 UTC | Fix doc line for remove_duplicates | 31 March 2015, 14:55:27 UTC |
| f4adb57 | Susanna Siebert | 31 March 2015, 14:54:07 UTC | Remove default values from doc line | 31 March 2015, 14:54:07 UTC |
| b4f6a12 | Susanna Siebert | 31 March 2015, 14:52:55 UTC | Remove unnecessary dereferencing | 31 March 2015, 14:52:55 UTC |
| 1b512a6 | Susanna Siebert | 31 March 2015, 14:50:31 UTC | Fix version in test message | 31 March 2015, 14:50:31 UTC |
| b13f3ec | Susanna Siebert | 31 March 2015, 14:49:22 UTC | Use qq instead of escaping quotes | 31 March 2015, 14:49:22 UTC |
| 9188c79 | Nathaniel Nutter | 24 March 2015, 21:10:44 UTC | add MigrateLockProxy A MigrateLockProxy object can be used to migrate a lock from one resource/scope to another. This will aid in fixing issues where the chosen resource turns out to be a poor choice, e.g. it's length exceeds that supported by a backend, and with migrating away from the `tgisan` and `unknown` scopes. | 31 March 2015, 14:10:12 UTC |
| 1693c8a | Nathaniel Nutter | 24 March 2015, 21:09:45 UTC | lift restriction on multiple scopes In order to migrate from one scope to another we must lift the restriction on one lock per resource across all scopes. | 31 March 2015, 14:10:06 UTC |
| 2839f63 | Nathaniel Nutter | 24 March 2015, 21:09:27 UTC | require scope on unlock_resource In order to remove the limitation on one per resource across all scopes we must first require `scope` on `unlock_resource`. | 31 March 2015, 14:10:04 UTC |
| f5a461a | Nathaniel Nutter | 30 March 2015, 21:03:14 UTC | convert PAP's UploadResult to LockProxy | 31 March 2015, 14:10:02 UTC |
| 3077092 | Nathaniel Nutter | 30 March 2015, 16:17:43 UTC | convert MetagenomicShotgun to LockProxy | 31 March 2015, 14:10:01 UTC |
| 441409e | Nathaniel Nutter | 30 March 2015, 16:17:24 UTC | convert MetagenomicCompositionShotgun to LockProxy | 31 March 2015, 14:09:59 UTC |
| 0f7564a | Nathaniel Nutter | 27 March 2015, 22:04:13 UTC | convert SoftwareResult::User to LockProxy | 31 March 2015, 14:09:57 UTC |
| ee7165c | Nathaniel Nutter | 27 March 2015, 22:03:29 UTC | convert SoftwareResult to LockProxy | 31 March 2015, 14:09:56 UTC |
| 3df3597 | Nathaniel Nutter | 27 March 2015, 22:02:15 UTC | convert ObjectWithLockedConstruction to LockProxy | 31 March 2015, 14:09:54 UTC |
| 7a3aa11 | Nathaniel Nutter | 27 March 2015, 22:01:25 UTC | convert SyncLimsAndGenome to LockProxy | 31 March 2015, 14:09:52 UTC |
| 65ed03b | Nathaniel Nutter | 27 March 2015, 22:00:23 UTC | convert Synchronize to LockProxy | 31 March 2015, 14:09:50 UTC |
