| b61b427 | dmorton | 29 June 2014, 03:48:59 UTC | Move Interpreter/Base to Component/Interpreter | 29 June 2014, 03:48:59 UTC |
| 0e14322 | dmorton | 29 June 2014, 03:33:15 UTC | Move Filter/Base to Component/Filter | 29 June 2014, 03:44:14 UTC |
| c435d03 | dmorton | 29 June 2014, 02:54:39 UTC | Move Expert/CommandBase to Component/Expert/Command | 29 June 2014, 02:54:39 UTC |
| 04e9c24 | dmorton | 29 June 2014, 02:48:19 UTC | Move Expert/CommandBase to Component/Expert/Command | 29 June 2014, 02:48:19 UTC |
| f80988c | dmorton | 29 June 2014, 02:18:04 UTC | Move Expert/Base to Component/Expert | 29 June 2014, 02:18:04 UTC |
| 4686682 | dmorton | 29 June 2014, 00:13:37 UTC | Moved AdaptorBase to Component/Adaptor | 29 June 2014, 00:31:08 UTC |
| 76b7bce | dmorton | 28 June 2014, 23:31:51 UTC | Moved ComponentBase to Component/Base | 28 June 2014, 23:31:51 UTC |
| f73710d | dmorton | 28 June 2014, 22:49:22 UTC | Move Plan.t and Plan-validate.t into Plan directory | 28 June 2014, 22:49:22 UTC |
| 97437f1 | Susanna Siebert | 27 June 2014, 16:00:40 UTC | updated netMHC package path | 27 June 2014, 16:00:40 UTC |
| 379afef | APipe Tester | 27 June 2014, 12:17:42 UTC | Updated `genome` tab completion. | 27 June 2014, 12:17:42 UTC |
| ceea59a | APipe Tester | 26 June 2014, 22:01:22 UTC | updated getopt-complete submodule to 2dc69f2 | 26 June 2014, 22:01:22 UTC |
| 6b93616 | APipe Tester | 26 June 2014, 22:00:50 UTC | updated ur submodule to 676e05b | 26 June 2014, 22:00:50 UTC |
| 528f95d | Feiyu Du | 26 June 2014, 21:25:12 UTC | add indel to test | 26 June 2014, 21:25:12 UTC |
| 9609e72 | Nathaniel Nutter | 26 June 2014, 20:38:51 UTC | builds validate instrument data bam_path has size | 26 June 2014, 20:38:51 UTC |
| 2365575 | Nathaniel Nutter | 26 June 2014, 20:36:11 UTC | InstrumentData needs an allocation to be valid | 26 June 2014, 20:36:43 UTC |
| 69ce4e6 | Nathaniel Nutter | 26 June 2014, 00:27:48 UTC | validate instrument data bam_path has size This might be overreaching on the base Genome::Model::Build class but it's definitely needed for anything that does BWA, BWAMEM, or BWASW alignment. For those types of alignment instrument data with a bam_path but no size results in an invalid Workflow model that cannot be commited to the DB. | 26 June 2014, 20:36:42 UTC |
| 4fc0cde | Nathaniel Nutter | 26 June 2014, 00:27:40 UTC | whitespace | 26 June 2014, 20:36:40 UTC |
| 3d64f31 | Thomas Mooney | 26 June 2014, 19:57:08 UTC | Use existing implementation of camel_case_to_string. Only override to get the error behaviour we're after. | 26 June 2014, 19:57:08 UTC |
| 52b7ba1 | Thomas Mooney | 26 June 2014, 19:55:42 UTC | Use existing method to get sub-command names. The alternative implementation was defective. It would not hyphenate commands appropriately. Rather than fix this one, use the one that commands use generally. | 26 June 2014, 19:55:42 UTC |
| c12dcda | Ian Ferguson | 26 June 2014, 19:01:52 UTC | Add bwa versions 0.7.8 and 0.7.9a to GMT::Bwa | 26 June 2014, 19:01:52 UTC |
| b2d01f0 | Adam Coffman | 26 June 2014, 18:44:32 UTC | changed date_scheduled to created_at in query | 26 June 2014, 18:44:32 UTC |
| 1726e9e | Thomas Mooney | 26 June 2014, 14:22:05 UTC | Blithely update expected output again. | 26 June 2014, 14:22:05 UTC |
| a98aaf6 | apregier | 25 June 2014, 20:40:59 UTC | Merge branch 'updated' into gb_master | 25 June 2014, 20:40:59 UTC |
| 1c8623a | apregier | 25 June 2014, 17:52:07 UTC | Add sift,polyphen, and condel to tumor-only report | 25 June 2014, 20:40:19 UTC |
| fde4524 | apregier | 24 June 2014, 21:12:33 UTC | Correctly query for deletions in bam readcount entries | 25 June 2014, 20:40:18 UTC |
| 5375eb0 | apregier | 24 June 2014, 20:16:48 UTC | Correctly query bam-readcount for insertion alleles | 25 June 2014, 20:40:17 UTC |
| 0018208 | Thomas Mooney | 25 June 2014, 19:36:49 UTC | Quiet undefined warnings. | 25 June 2014, 19:36:49 UTC |
| 6fc25d6 | Thomas Mooney | 25 June 2014, 19:17:52 UTC | Don't try to re-purge purged allocations. | 25 June 2014, 19:17:52 UTC |
| 5ad5ae3 | Eddie Belter | 25 June 2014, 17:11:26 UTC | Build Cmds: uses associated_disk_allocations instaed of all_allocations | 25 June 2014, 17:32:49 UTC |
| 43baedd | Eddie Belter | 25 June 2014, 17:11:26 UTC | Build Unarchive: uses associated_disk_allocations instaed of all_allocations | 25 June 2014, 17:11:57 UTC |
| b5dfae3 | APipe Tester | 25 June 2014, 12:17:11 UTC | Updated `genome` tab completion. | 25 June 2014, 12:17:11 UTC |
| 5ee871d | APipe Tester | 25 June 2014, 12:15:35 UTC | Updated class browser cache. | 25 June 2014, 12:15:35 UTC |
| 97d44e5 | dmorton | 24 June 2014, 22:55:42 UTC | Clean up unneeded code This was implemented before the use of Memoize library but wasn't removed once Memoize was utilized | 24 June 2014, 22:56:36 UTC |
| e2c5257 | dmorton | 24 June 2014, 22:54:52 UTC | Add test that covers problem with using tmp file path as SR input | 24 June 2014, 22:56:36 UTC |
| 61f4989 | dmorton | 24 June 2014, 17:06:13 UTC | Ensure that ConvertedBedResults can shortcut They were prviously being provided with tmp file paths as an input, which would never allow them to shortcut. | 24 June 2014, 22:56:36 UTC |
| c0bf6c2 | Eddie Belter | 24 June 2014, 20:43:44 UTC | GM: reader factory unarchives instdata if archived | 24 June 2014, 21:34:16 UTC |
| 08b067d | Eddie Belter | 24 June 2014, 20:42:24 UTC | Test Factory: imported inst data uses disk alloc factory | 24 June 2014, 21:34:15 UTC |
| d65c9d4 | Eddie Belter | 24 June 2014, 20:39:44 UTC | Test Factory: disk allocation archive stores the mount path; unarchive sets the previous mount path or new temp one | 24 June 2014, 21:34:15 UTC |
| 78c7f27 | Eddie Belter | 23 June 2014, 19:12:39 UTC | Build: add _unarchive_disk_allocations method that calls unarchive command for use with objects w/ allocations | 24 June 2014, 21:34:14 UTC |
| 6c01570 | Eddie Belter | 19 June 2014, 13:39:45 UTC | GM: remove commented out lines in test module | 24 June 2014, 21:34:14 UTC |
| b364b17 | Eddie Belter | 24 June 2014, 20:58:21 UTC | Hmp: rmove unused test | 24 June 2014, 20:58:57 UTC |
| 70adc12 | Nathaniel Nutter | 24 June 2014, 20:27:40 UTC | remove unused argument As far as I could tell this argument doesn't get used and may have been a copy-paste from the Cache version. | 24 June 2014, 20:38:30 UTC |
| 68942c3 | Nathaniel Nutter | 24 June 2014, 20:27:04 UTC | move 'path' argument to PSGI env Plack::Middleware do not pass on arguments, only the PSGI env, so to be compatible with Plack::Middleware we need an alternative to arguments. I don't know if this is the correct solution but it seems to work. | 24 June 2014, 20:38:30 UTC |
| d47b024 | Nathaniel Nutter | 24 June 2014, 20:24:31 UTC | move 'ajax_refresh' argument to PSGI env Plack::Middleware do not pass on arguments, only the PSGI env, so to be compatible with Plack::Middleware we need an alternative to arguments. I don't know if this is the correct solution but it seems to work. | 24 June 2014, 20:38:29 UTC |
| cb0c34b | Eddie Belter | 24 June 2014, 20:34:26 UTC | InstData Import: mv HMP commands to Site/TGI/Hmp | 24 June 2014, 20:35:20 UTC |
| c499117 | Eddie Belter | 04 June 2014, 22:00:18 UTC | InstData: rename headers var in generate file for reimport | 24 June 2014, 20:35:18 UTC |
| 2d06de4 | Eddie Belter | 04 June 2014, 21:58:13 UTC | InstData: fix reimport class name; add reimported_from method | 24 June 2014, 20:35:17 UTC |
| ed19641 | Eddie Belter | 04 June 2014, 21:43:34 UTC | InstData: add reimport helper class; use it in generate file for reimport | 24 June 2014, 20:35:17 UTC |
| 4c470f7 | Eddie Belter | 04 June 2014, 21:33:00 UTC | InstData: mv generate source files tsv to base command dir; remove most references to source files | 24 June 2014, 20:35:16 UTC |
| 0522f6a | Eddie Belter | 04 June 2014, 21:12:06 UTC | InstData Import: command to generate tsv file to reimport | 24 June 2014, 20:35:15 UTC |
| be76916 | Thomas Mooney | 24 June 2014, 15:39:18 UTC | New command to show config (mis)matches for an instrument-data | 24 June 2014, 15:39:18 UTC |
| 9114971 | APipe Tester | 24 June 2014, 12:17:02 UTC | Updated `genome` tab completion. | 24 June 2014, 12:17:02 UTC |
| baccbc0 | Nathaniel Nutter | 23 June 2014, 22:24:24 UTC | delegate permission changes to allocation | 23 June 2014, 22:27:40 UTC |
| 82175ba | Nathaniel Nutter | 23 June 2014, 22:19:17 UTC | add set_files_read_only (as opposed to files and directories) | 23 June 2014, 22:27:39 UTC |
| 71e5381 | Nathaniel Nutter | 23 June 2014, 22:18:55 UTC | add alias for function | 23 June 2014, 22:27:38 UTC |
| dc9fda7 | Thomas Mooney | 23 June 2014, 20:46:51 UTC | Update ClinSeq to account for DGIdb changes. | 23 June 2014, 20:46:51 UTC |
| 1a890a9 | Nathaniel Nutter | 23 June 2014, 20:12:22 UTC | add --unstartable-ok option In BQM unstartable "failures" do not need to result in an error since they are monitored downstream. Using this option will keep BQM from turning red when there are unstartable builds. | 23 June 2014, 20:12:22 UTC |
| 3cca138 | Thomas Mooney | 23 June 2014, 18:14:32 UTC | Merge the keys of the response hash instead of overwriting them | 23 June 2014, 18:14:32 UTC |
| 7a6de6e | Jim Weible | 23 June 2014, 15:22:59 UTC | allow 0 sized output files | 23 June 2014, 15:22:59 UTC |
| fe60d05 | Steve Wilkerson | 20 June 2014, 21:41:41 UTC | Added additional fields for report | 20 June 2014, 21:42:48 UTC |
| 57953aa | Nathaniel Nutter | 20 June 2014, 14:25:11 UTC | fix not telling Perl that string was an octal number | 20 June 2014, 14:25:39 UTC |
| a7791f6 | APipe Tester | 20 June 2014, 12:17:59 UTC | Updated `gmt` tab completion. | 20 June 2014, 12:17:59 UTC |
| fc3889e | APipe Tester | 20 June 2014, 12:17:16 UTC | Updated `genome` tab completion. | 20 June 2014, 12:17:16 UTC |
| 3b57be9 | APipe Tester | 20 June 2014, 12:15:42 UTC | Updated class browser cache. | 20 June 2014, 12:15:42 UTC |
| 04e44d4 | Thomas Mooney | 20 June 2014, 03:27:15 UTC | Allow output_dir to be specified as input. The command already offers output_dir as a command-line option, but any supplied value was ignored. Now it will be used if provided. | 20 June 2014, 03:27:15 UTC |
| 3b0b768 | Thomas Mooney | 20 June 2014, 03:23:38 UTC | Fix test--fill in param to get_response. | 20 June 2014, 03:23:38 UTC |
| c7a9112 | Thomas Mooney | 20 June 2014, 03:16:15 UTC | whitespace | 20 June 2014, 03:16:15 UTC |
| e43a0f1 | Thomas Mooney | 20 June 2014, 03:13:43 UTC | Set batch query size to avoid server timeout. | 20 June 2014, 03:13:43 UTC |
| e37491a | Thomas Mooney | 20 June 2014, 03:12:59 UTC | Include server error in error message on failure. | 20 June 2014, 03:12:59 UTC |
| 5cba95d | dmorton | 19 June 2014, 23:25:54 UTC | Only clean up locks that you create Locks created before a fork/exec had the potential to be cleaned up after the fork but before the exec if the forked child died. Now we just store the pid of the process when the lock is created and ensure that it is the same process that cleans up the lock. | 20 June 2014, 00:29:44 UTC |
| 8ab464e | Nathaniel Nutter | 19 June 2014, 22:41:08 UTC | remove development environment option from local web-app According to `plackup` docs the 'development' environment just enables three middleware. One of those is AccessLog and since we are adding our own custom version of AccessLog we need to disable the original. The production server also enabled the 'development' environment and will need the same change. | 19 June 2014, 22:44:06 UTC |
| c91b092 | Nathaniel Nutter | 19 June 2014, 22:37:57 UTC | add custom logging middleware This adds to Plack::Middleware to our web app: - GenomeAccessLog is a copy of AccessLog with the PID added. This will allow us to connect a response to a worker PID. - GenomePreAccessLog is a fork of AccessLog to log requests before running the PSGI app. This will allow us to know what a worker is doing before the request completes. | 19 June 2014, 22:44:05 UTC |
| 9a46a8f | APipe Tester | 19 June 2014, 21:35:24 UTC | updated jenkins submodule to 5b180ee | 19 June 2014, 21:35:29 UTC |
| b6ad270 | APipe Tester | 19 June 2014, 21:35:08 UTC | updated ur submodule to 95c1411 | 19 June 2014, 21:35:28 UTC |
| 5434c41 | apregier | 19 June 2014, 21:35:18 UTC | Merge branch 'updated' into gb_master | 19 June 2014, 21:35:18 UTC |
| 37eaec3 | apregier | 19 June 2014, 21:34:06 UTC | Remove unneeded sub::install | 19 June 2014, 21:34:06 UTC |
| 563417c | Feiyu Du | 19 June 2014, 21:14:05 UTC | make G::VR::E::BamReadcout::RunResult produce the correct region list to feed to bam-readcount | 19 June 2014, 21:14:05 UTC |
| 1867c35 | Nathaniel Nutter | 19 June 2014, 19:02:56 UTC | use is_near_soft_limit instead of is_over_soft_limit To avoid allocations "flapping", i.e. create and rollback, when volumes are approaching soft limit we will disable them when they get "close enough". | 19 June 2014, 19:53:22 UTC |
| 40e7c61 | Nathaniel Nutter | 19 June 2014, 19:01:54 UTC | add method to dynamically define proximity to soft limit | 19 June 2014, 19:53:22 UTC |
| b634b4e | Nathaniel Nutter | 19 June 2014, 19:00:24 UTC | update allocated_kb to also return allocation count in list context | 19 June 2014, 19:53:21 UTC |
| be83206 | Nathaniel Nutter | 18 June 2014, 19:26:58 UTC | add cached_unallocated_kb and use instead of unallocated_kb | 19 June 2014, 19:53:21 UTC |
| b6bf8d3 | Nathaniel Nutter | 18 June 2014, 19:17:02 UTC | add metric to record the number of attempted volumes | 19 June 2014, 19:53:20 UTC |
| a0d9d92 | Nathaniel Nutter | 18 June 2014, 19:08:48 UTC | convert debug_message to Genome::Logger Convert debug_message to Genome::Logger so that they go to logstash. | 19 June 2014, 19:53:19 UTC |
| 58f2914 | Nathaniel Nutter | 18 June 2014, 19:05:32 UTC | make has_space also check used_kb to reduce rollbacks due to over_used | 19 June 2014, 19:53:19 UTC |
| 0ad0e36 | Nathaniel Nutter | 18 June 2014, 19:03:04 UTC | add some convience methods to check proximity of soft/hard limits | 19 June 2014, 19:53:18 UTC |
| 3ad40be | Ian Ferguson | 19 June 2014, 18:48:53 UTC | Modify Picard and Bwamem memory handling | 19 June 2014, 18:49:31 UTC |
| 4134083 | Jason Walker | 19 June 2014, 18:48:21 UTC | Add a common model_identifier param so results are consistent for SummarizeAnalysisProject | 19 June 2014, 18:48:21 UTC |
| a8ca55a | Jason Walker | 19 June 2014, 18:46:40 UTC | Add support for either paired-end or fragment data | 19 June 2014, 18:46:40 UTC |
| 9500510 | Jason Walker | 19 June 2014, 18:45:00 UTC | Add command to list per instrument data alignment BAM files | 19 June 2014, 18:45:00 UTC |
| d54e27d | Jason Walker | 19 June 2014, 18:44:13 UTC | Add methods to retrive per-instrument data BAM files from merged alignment result. | 19 June 2014, 18:44:13 UTC |
| 4a17ecc | apregier | 19 June 2014, 16:22:29 UTC | Merge branch 'updated' into gb_master | 19 June 2014, 16:22:29 UTC |
| 7b0ba1b | apregier | 16 June 2014, 22:11:22 UTC | Add debug message | 19 June 2014, 16:18:51 UTC |
| c499d7b | apregier | 16 June 2014, 18:45:53 UTC | No filter value should pass | 19 June 2014, 16:18:50 UTC |
| 3fae48e | Thomas Mooney | 19 June 2014, 15:36:29 UTC | Limit genotypes processed in a single run. When too many are backlogged the process times out. | 19 June 2014, 15:36:29 UTC |
| 6a10067 | Thomas Mooney | 19 June 2014, 15:35:51 UTC | Add LSF resource request to SNV-Indel Report | 19 June 2014, 15:35:51 UTC |
| c129595 | Susanna Siebert | 19 June 2014, 15:01:36 UTC | Merge branch 'epitope_prediction' | 19 June 2014, 15:01:36 UTC |
| 11e286a | Susanna Siebert | 19 June 2014, 14:14:23 UTC | pull annotation db name and version from the somatic variation build, if provided | 19 June 2014, 14:14:23 UTC |
| 8247f51 | Thomas Mooney | 19 June 2014, 13:37:03 UTC | Remove stray ' after table name. | 19 June 2014, 13:37:03 UTC |
| 235c50b | APipe Tester | 19 June 2014, 12:17:39 UTC | Updated `genome` tab completion. | 19 June 2014, 12:17:39 UTC |
| a3dec5c | APipe Tester | 19 June 2014, 12:15:53 UTC | Updated class browser cache. | 19 June 2014, 12:15:53 UTC |
