| 4f8baa8 | Thomas Mooney | 20 March 2013, 14:37:19 UTC | Add support for packaged picard-tools versions under /usr/share/java/. | 20 March 2013, 14:37:19 UTC |
| 239dfb7 | nnutter | 20 March 2013, 03:58:14 UTC | additional cleanup | 20 March 2013, 04:13:08 UTC |
| fcd13f1 | nnutter | 20 March 2013, 03:47:16 UTC | data_dir changes - split into separate data_dir - support optional test version - validate package | 20 March 2013, 04:13:07 UTC |
| fb6213c | Scott Smith | 20 March 2013, 04:07:05 UTC | updated docs on htseq | 20 March 2013, 04:07:05 UTC |
| 21f0d31 | Scott Smith | 20 March 2013, 03:22:44 UTC | ensure the display of alignment results includes the test name | 20 March 2013, 03:22:44 UTC |
| 580af2a | nnutter | 20 March 2013, 00:13:32 UTC | refactor, no feature changes | 20 March 2013, 00:34:16 UTC |
| 8bd58ca | nnutter | 20 March 2013, 00:12:44 UTC | formalize file order: got, expected - invert diff so it's relative to second/expected file - rename vars to indicate expected - place expected in correct position | 20 March 2013, 00:33:35 UTC |
| 28b8a1e | nnutter | 19 March 2013, 23:24:05 UTC | cleanup test | 20 March 2013, 00:16:58 UTC |
| 83f6207 | nnutter | 19 March 2013, 23:23:26 UTC | add data_dir_ok | 20 March 2013, 00:16:57 UTC |
| 3465523 | nnutter | 19 March 2013, 23:02:35 UTC | builder is supposed to be called in functions not just once | 20 March 2013, 00:16:57 UTC |
| 7da90b3 | nnutter | 19 March 2013, 23:01:25 UTC | cleanup | 20 March 2013, 00:16:56 UTC |
| 0d98d46 | nnutter | 19 March 2013, 23:01:08 UTC | add replace option for compare_ok | 20 March 2013, 00:16:56 UTC |
| 09f2780 | APipe Tester | 19 March 2013, 21:35:49 UTC | updated ur submodule to 22f91bc | 19 March 2013, 21:35:49 UTC |
| cfa2ab1 | Adam Coffman | 19 March 2013, 19:57:35 UTC | add get_all_allocations_for_path method | 19 March 2013, 19:57:35 UTC |
| 36ac5c7 | Scott Smith | 19 March 2013, 19:01:20 UTC | updated merge logic for Genome::Command::WithSavedResults, and updated the HTSeq implementation | 19 March 2013, 19:01:20 UTC |
| 59e4b96 | Thomas Mooney | 19 March 2013, 18:42:53 UTC | Remove color codes from EOLs of expected output. | 19 March 2013, 18:42:53 UTC |
| a4130b2 | Kyung Kim | 19 March 2013, 17:07:45 UTC | update to create cleaned scaffolds.fasta that matches metrics | 19 March 2013, 17:07:45 UTC |
| ddfda17 | APipe Tester | 19 March 2013, 16:21:07 UTC | Updated `genome` tab completion. | 19 March 2013, 16:21:07 UTC |
| 8736045 | APipe Tester | 19 March 2013, 16:14:18 UTC | Updated `genome` tab completion. | 19 March 2013, 16:15:24 UTC |
| ea1c282 | APipe Tester | 19 March 2013, 16:07:32 UTC | updated ur submodule to 491b87b | 19 March 2013, 16:07:32 UTC |
| 5a0edb6 | Thomas Mooney | 19 March 2013, 13:53:14 UTC | Automatically decide the number of threads to use for PerLaneTophat. | 19 March 2013, 13:53:14 UTC |
| f511fc7 | Adam Coffman | 18 March 2013, 23:11:29 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 18 March 2013, 23:11:29 UTC |
| f9d70b7 | Adam Coffman | 18 March 2013, 23:11:21 UTC | add get_active_volume method to volume | 18 March 2013, 23:11:21 UTC |
| b76f661 | dmorton | 18 March 2013, 22:50:55 UTC | use arrow instead of . (PERL is not Python) | 18 March 2013, 22:50:55 UTC |
| 21c1796 | dmorton | 18 March 2013, 22:09:50 UTC | Merge branch 'ChimerascanBase' | 18 March 2013, 22:09:50 UTC |
| d33163f | dmorton | 15 March 2013, 15:39:04 UTC | Fix instrument_data->bam_file to be bam_path | 18 March 2013, 21:44:13 UTC |
| 43b9764 | dmorton | 08 March 2013, 18:18:33 UTC | Make ChimerascanResult use ChimerascanBase | 18 March 2013, 21:44:13 UTC |
| 843bc99 | dmorton | 08 March 2013, 18:17:20 UTC | Stop using build->model->x in Chimerascan command | 18 March 2013, 21:44:12 UTC |
| d67929e | dmorton | 08 March 2013, 18:16:18 UTC | Made ChimerascanBase Class | 18 March 2013, 21:44:12 UTC |
| 762dc8b | dmorton | 07 March 2013, 16:50:37 UTC | Added back in the old Chimerascan (not vrl) | 18 March 2013, 21:44:12 UTC |
| 2482a18 | Brian Derickson | 18 March 2013, 21:01:42 UTC | use rmdir instead of Genome::Sys->remove_directory_tree | 18 March 2013, 21:03:44 UTC |
| fb2a015 | Brian Derickson | 18 March 2013, 20:44:56 UTC | Changes to CreateForExisting allocation command Renamed to import. Primitivized method arguments for easier testing. | 18 March 2013, 21:03:44 UTC |
| 41501aa | Eddie Belter | 18 March 2013, 18:25:21 UTC | MetaShot: extract unaligned from meta nr | 18 March 2013, 20:14:32 UTC |
| 31b927b | Eddie Belter | 18 March 2013, 18:19:22 UTC | MetaShot: align to - consolidate some methods, rm dies | 18 March 2013, 20:14:32 UTC |
| b928764 | Eddie Belter | 15 March 2013, 15:16:40 UTC | MetaShot: build if necessary takes only one model; rm commit | 18 March 2013, 20:14:32 UTC |
| 9f5b327 | Eddie Belter | 15 March 2013, 15:10:41 UTC | MetaShot: separate assign inst data and build in align to | 18 March 2013, 20:14:31 UTC |
| d5fcde4 | Eddie Belter | 15 March 2013, 14:40:44 UTC | MetaShot: update align to to use inst data assign/unassign command to add/rm inst data | 18 March 2013, 20:14:31 UTC |
| 801efae | dmorton | 18 March 2013, 19:23:04 UTC | Fix gmb view for builds with no results. | 18 March 2013, 19:26:28 UTC |
| 8056b86 | apregier | 18 March 2013, 18:25:57 UTC | Sleep before retry | 18 March 2013, 18:25:57 UTC |
| f9d09b3 | apregier | 18 March 2013, 17:02:37 UTC | Report/Email.pm | 18 March 2013, 18:12:28 UTC |
| 7f07900 | apregier | 18 March 2013, 16:15:00 UTC | Build with no results can still be viewed | 18 March 2013, 16:15:33 UTC |
| 55d0b63 | APipe Tester | 18 March 2013, 16:13:11 UTC | Updated `gmt` tab completion. | 18 March 2013, 16:13:11 UTC |
| 4eb7c45 | APipe Tester | 18 March 2013, 16:12:08 UTC | Updated `genome` tab completion. | 18 March 2013, 16:12:08 UTC |
| afbd9eb | APipe Tester | 18 March 2013, 16:05:08 UTC | Updated `gmt` tab completion. | 18 March 2013, 16:05:10 UTC |
| 78b7fb5 | APipe Tester | 18 March 2013, 16:04:06 UTC | Updated `genome` tab completion. | 18 March 2013, 16:05:10 UTC |
| 51a074c | apregier | 18 March 2013, 15:53:33 UTC | Merge branch 'fireteam2' into gb_master | 18 March 2013, 15:53:33 UTC |
| 06126ae | apregier | 18 March 2013, 15:48:40 UTC | Fix table names for ucsc gap-list | 18 March 2013, 15:48:40 UTC |
| f18e957 | nnutter | 16 March 2013, 05:31:18 UTC | fix for when there are no changed perl files | 16 March 2013, 05:31:18 UTC |
| 072877e | APipe Tester | 16 March 2013, 04:08:13 UTC | updated workflow submodule to a730105 | 16 March 2013, 04:08:13 UTC |
| 88c984a | apregier | 15 March 2013, 23:17:18 UTC | Merge branch 'updated2' into gb_master | 15 March 2013, 23:17:18 UTC |
| 5d504e7 | apregier | 15 March 2013, 23:16:55 UTC | Remove amplicon assembly from summary of builds test | 15 March 2013, 23:17:04 UTC |
| 332c02e | nnutter | 15 March 2013, 23:07:46 UTC | Merge branch 'perl-tests' | 15 March 2013, 23:07:46 UTC |
| 95a6f69 | nnutter | 15 March 2013, 23:06:56 UTC | 135722070 was approved by Malachi Griffith | 15 March 2013, 23:06:56 UTC |
| 270c0b1 | apregier | 15 March 2013, 21:42:26 UTC | Merge branch 'updated2' into gb_master | 15 March 2013, 21:42:26 UTC |
| 36e07ee | apregier | 15 March 2013, 21:26:53 UTC | Remove Amplicon Assembly | 15 March 2013, 21:42:06 UTC |
| 1b2c238 | Ian Ferguson | 15 March 2013, 19:56:11 UTC | More checks in Allocation::CreateForExistingData Additional checks for `genome disk allocation create-for-existing-data`. It now makes sure that the provided target path has an identical absolute path (this prevents paths with things like '..'). Also makes sure that the target path is not a symlink. Added test coverage. | 15 March 2013, 20:19:07 UTC |
| 542c3ca | Brian Derickson | 13 March 2013, 22:04:53 UTC | better handling of temp allocation location Temp location is now stored on the command object as a transient property. This path is also cleaned up prior to exiting. Also added checks on parent/child allocations. Test has been expanded to cover all these cases. | 15 March 2013, 20:19:06 UTC |
| 5219e4b | Brian Derickson | 13 March 2013, 17:56:21 UTC | command for creating allocations for existing data Creates an allocation right next to existing data and then updates the allocation path. This is safer than a direct create because that process will delete the allocation path in case of failure, wiping out any data that was there. Also includes a test for this command. | 15 March 2013, 20:19:06 UTC |
| a8214ae | apregier | 15 March 2013, 20:12:35 UTC | Merge branch 'updated2' into gb_master | 15 March 2013, 20:12:35 UTC |
| c2a2052 | apregier | 15 March 2013, 20:11:56 UTC | Bless clinseq build | 15 March 2013, 20:11:56 UTC |
| 7b5df0e | apregier | 15 March 2013, 20:09:54 UTC | Switch to File::Next File::Find only gets files in a symlinked directory once, even if the directory is symlinked multiple times. | 15 March 2013, 20:11:21 UTC |
| a290272 | Ian Ferguson | 15 March 2013, 19:01:06 UTC | More descriptive reallocation status messages. | 15 March 2013, 19:01:06 UTC |
| 694d2be | Ian Ferguson | 15 March 2013, 18:37:22 UTC | Read generation for PerLaneTophat aligner index Genome::InstrumentData::AlignmentResult::PerLaneTophat requires several 'fake' reads during index creation. We previously had 3 hard-coded sequences taken from the human reference, but this caused the command used for index creation to give a non-zero exit status when run against a reference that did not have these sequences. Instead of trying to verify that the index was created despite the exit status, we now generate 50 additional fake reads that are appropriate for the provided reference and annotation. | 15 March 2013, 18:37:22 UTC |
| 5532891 | nnutter | 15 March 2013, 17:50:47 UTC | show $Mail::Sender::Error if it is set | 15 March 2013, 17:52:31 UTC |
| 5684ab8 | Dan Koboldt | 15 March 2013, 17:10:21 UTC | Removed default values for reference | 15 March 2013, 17:10:21 UTC |
| 3f91b39 | Dan Koboldt | 15 March 2013, 17:03:36 UTC | Removed filesystem default | 15 March 2013, 17:03:36 UTC |
| 6fb7ee0 | dmorton | 15 March 2013, 16:04:28 UTC | Add logic to show SoftwareResult Test Name in gmb view | 15 March 2013, 16:04:28 UTC |
| ddd1e99 | dmorton | 14 March 2013, 22:54:56 UTC | gmb view now shows calculated elapsed times in color | 15 March 2013, 15:40:52 UTC |
| 8f7fe6f | nnutter | 15 March 2013, 05:41:28 UTC | rename function to reflect fact that it does not perform a test | 15 March 2013, 05:41:28 UTC |
| 7106e10 | nnutter | 15 March 2013, 05:13:34 UTC | shouldn't `do` a test | 15 March 2013, 05:13:43 UTC |
| 173e5bf | nnutter | 15 March 2013, 04:09:06 UTC | test_fail does not work when wrapped in a `do` (test-tracker) | 15 March 2013, 04:09:06 UTC |
| 5ddae02 | nnutter | 14 March 2013, 20:44:12 UTC | add test to replace `ur test use` | 14 March 2013, 21:44:23 UTC |
| 05ff49e | nnutter | 14 March 2013, 20:56:35 UTC | limit test tracking | 14 March 2013, 21:44:22 UTC |
| 89c9d83 | nnutter | 14 March 2013, 20:43:39 UTC | whitespace | 14 March 2013, 21:44:22 UTC |
| 60280da | APipe Tester | 14 March 2013, 20:32:04 UTC | updated jenkins submodule to 3319447 | 14 March 2013, 20:32:04 UTC |
| 1657cf3 | APipe Tester | 14 March 2013, 20:31:57 UTC | updated ur submodule to 6521360 | 14 March 2013, 20:31:57 UTC |
| 19f8e29 | apregier | 14 March 2013, 20:12:36 UTC | Merge branch 'updated2' into gb_master | 14 March 2013, 20:12:36 UTC |
| 8f33a8f | apregier | 14 March 2013, 20:12:17 UTC | Removed obsolete model tests | 14 March 2013, 20:12:17 UTC |
| 033022d | apregier | 14 March 2013, 19:30:51 UTC | Merge branch 'updated2' into gb_master | 14 March 2013, 19:30:51 UTC |
| 8f9bcc2 | apregier | 14 March 2013, 19:30:14 UTC | Test shouldn't write into test data dir | 14 March 2013, 19:30:14 UTC |
| 25dfe01 | apregier | 14 March 2013, 19:07:25 UTC | Merge branch 'updated2' into gb_master | 14 March 2013, 19:07:25 UTC |
| 0dcd129 | apregier | 14 March 2013, 19:06:46 UTC | Test should not overwrite files in test data directory | 14 March 2013, 19:06:46 UTC |
| 1037680 | apregier | 14 March 2013, 17:49:06 UTC | Merge branch 'updated2' into gb_master | 14 March 2013, 17:49:06 UTC |
| d08d6b8 | apregier | 14 March 2013, 15:36:29 UTC | Remove unused somatic pipeline tools Remove unused somatic pipeline stuff Fix some tests that depended on somatic models | 14 March 2013, 17:48:42 UTC |
| 1cf812b | Dave Larson | 13 March 2013, 16:31:12 UTC | change name to indicate only working on wgs | 14 March 2013, 17:15:39 UTC |
| 3fc48b1 | Dave Larson | 13 March 2013, 16:29:29 UTC | tool to plot clonality by source from wgs data is functional. needs tests and some refactoring | 14 March 2013, 17:15:39 UTC |
| 80686c9 | Dave Larson | 11 March 2013, 03:29:53 UTC | begin stubin of tool to graph clonality per each caller. | 14 March 2013, 17:15:38 UTC |
| 33352bc | Scott Smith | 14 March 2013, 16:14:55 UTC | update to not throw exceptions when possibly extending Command::V1 | 14 March 2013, 16:14:55 UTC |
| ecc0110 | Scott Smith | 14 March 2013, 15:09:34 UTC | make Genome::SoftwareResult::Default delegate to the command for disk group and disk allocation subdirectory when implemented | 14 March 2013, 15:09:34 UTC |
| cb5900b | Scott Smith | 14 March 2013, 15:06:15 UTC | ensure we don't try to make extensions for Command::V1 as before ...fixes test which expects this | 14 March 2013, 15:06:48 UTC |
| 3e6d303 | Mark Burnett | 14 March 2013, 14:11:13 UTC | Merge branch 'compare_usage' | 14 March 2013, 14:11:13 UTC |
| b63f419 | Mark Burnett | 14 March 2013, 14:03:51 UTC | add command: genome disk allocation compare-usage This command generates a CSV for comparing kilobytes_requested with kilobytes_used. | 14 March 2013, 14:05:22 UTC |
| ac9e2e7 | Mark Burnett | 13 March 2013, 19:58:31 UTC | die when checking `du` on an archived disk allocation | 14 March 2013, 14:05:21 UTC |
| ea4c7e4 | Mark Burnett | 13 March 2013, 19:50:57 UTC | cache Disk::Allocation->du results during reallocate | 14 March 2013, 14:05:21 UTC |
| d885eec | Mark Burnett | 13 March 2013, 19:00:53 UTC | add Disk::Allocation->du() | 14 March 2013, 14:05:20 UTC |
| 1686d71 | Eddie Belter | 14 March 2013, 00:12:49 UTC | MC16s: update tests for workflow changes | 14 March 2013, 00:12:57 UTC |
| 72533e0 | Eddie Belter | 13 March 2013, 23:30:03 UTC | MC16s: update workflow input and output build handling | 14 March 2013, 00:12:57 UTC |
| a3c106a | Eddie Belter | 14 March 2013, 00:12:14 UTC | MetaShot: fixes to get a model to short cut successfully! | 14 March 2013, 00:12:14 UTC |
| ac6c321 | apregier | 13 March 2013, 19:45:50 UTC | Merge branch 'fireteam2' into gb_master | 13 March 2013, 19:45:50 UTC |
| f1a9268 | apregier | 13 March 2013, 19:42:30 UTC | Add gatk-protected to vendor | 13 March 2013, 19:44:05 UTC |
