| 52c851f | apregier | 27 March 2013, 14:54:17 UTC | Fix typo | 27 March 2013, 14:54:30 UTC |
| 07dedd5 | nnutter | 27 March 2013, 04:05:54 UTC | fix alarm | 27 March 2013, 04:05:54 UTC |
| bc74aeb | nnutter | 27 March 2013, 02:51:50 UTC | Merge branch 'update_classes' This is all prep work for upcoming UR changes and for running `ur update classes-from-db`. | 27 March 2013, 02:51:50 UTC |
| aa59f2e | nnutter | 26 March 2013, 22:27:20 UTC | only add wingspan option to command if defined | 27 March 2013, 02:51:41 UTC |
| 5f3419e | nnutter | 08 March 2013, 15:49:22 UTC | sort section in preperation for update classes-from-db | 27 March 2013, 02:51:41 UTC |
| ad65b53 | Nathan Nutter | 28 February 2013, 16:28:05 UTC | property without column should be marked transient | 27 March 2013, 02:51:40 UTC |
| 4dbacf2 | nnutter | 06 March 2013, 21:09:05 UTC | add missing my | 27 March 2013, 02:51:40 UTC |
| 3e9011b | nnutter | 05 March 2013, 22:55:08 UTC | fix case where no PATHS_TO_REMOVE | 27 March 2013, 02:51:40 UTC |
| c2bcbc3 | Nathan Nutter | 01 March 2013, 00:35:25 UTC | ignore two more tables | 27 March 2013, 02:51:39 UTC |
| 37eb1f8 | Nathan Nutter | 27 February 2013, 21:03:29 UTC | trying to hide class from UR | 27 March 2013, 02:51:39 UTC |
| d735d00 | nnutter | 26 March 2013, 21:13:53 UTC | pre-fix for dependency on UR bug This currently depends on a bug in UR that will soon be fixed and will then need to fall back onto Workflow::DataSource::InstanceSchema as a consequence of our Postgres/Oracle syncing. | 27 March 2013, 02:51:38 UTC |
| dbad428 | Nathan Nutter | 27 February 2013, 21:41:04 UTC | move _ignore_table back to GMSchema | 27 March 2013, 02:51:38 UTC |
| 66752a1 | Nathan Nutter | 27 February 2013, 21:40:23 UTC | whitespace | 27 March 2013, 02:51:37 UTC |
| 97a248b | nnutter | 26 March 2013, 20:44:00 UTC | fix directories being made without group write due to restricted umask | 27 March 2013, 01:09:19 UTC |
| 3e2d435 | apregier | 26 March 2013, 23:23:57 UTC | Move references to the cancer gene list to dbpath | 26 March 2013, 23:23:57 UTC |
| ee6c34d | apregier | 26 March 2013, 21:44:06 UTC | Add documentation for annotate sv | 26 March 2013, 21:44:13 UTC |
| 5bafd53 | APipe Tester | 26 March 2013, 21:11:48 UTC | updated workflow submodule to ea4a2bf | 26 March 2013, 21:11:48 UTC |
| 22e70f4 | Jasreet Hundal | 26 March 2013, 20:38:15 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 26 March 2013, 20:38:15 UTC |
| 773eab0 | Jasreet Hundal | 26 March 2013, 20:38:06 UTC | removed debugging print statements | 26 March 2013, 20:38:06 UTC |
| f9a3565 | Ben Oberkfell | 26 March 2013, 20:28:52 UTC | Merge branch 'master' of git:/srv/git/genome | 26 March 2013, 20:28:52 UTC |
| b5b7c2a | Ben Oberkfell | 26 March 2013, 20:28:19 UTC | CHANGELOG: Tighter coupling of timing of Postgres & Oracle commits. Register a commit callback on the Oracle side to wait until Postgres has fully committed. Intent is to reduce race conditions in instances where shell commands are called that create entities that are queried for right away. For example, allocations. | 26 March 2013, 20:28:24 UTC |
| d4bc7f0 | Feiyu Du | 26 March 2013, 20:20:15 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 26 March 2013, 20:20:15 UTC |
| 11885d0 | Feiyu Du | 26 March 2013, 20:20:07 UTC | Blessing som-var-sv-detection build test for new sv annotation | 26 March 2013, 20:20:07 UTC |
| e6080c7 | Eddie Belter | 26 March 2013, 19:48:38 UTC | Solexa: add read trimmer version to all single SX comands if present | 26 March 2013, 19:48:47 UTC |
| d608a91 | Feiyu Du | 26 March 2013, 19:05:40 UTC | Blessing som-var-short build test for new sv annotation | 26 March 2013, 19:05:40 UTC |
| 9d28b85 | Feiyu Du | 25 March 2013, 19:42:46 UTC | syntax error fixed | 26 March 2013, 15:58:57 UTC |
| 996088d | Feiyu Du | 22 March 2013, 20:40:36 UTC | More update to plug new sv annotation to som var pipeline | 26 March 2013, 15:58:57 UTC |
| 3c16b47 | Feiyu Du | 20 March 2013, 15:32:58 UTC | Implement new sv annotation into somatic variation pipeline | 26 March 2013, 15:58:56 UTC |
| b2afc2c | Thomas Mooney | 26 March 2013, 15:28:57 UTC | Stop sending mail every minute when there's nothing to build. | 26 March 2013, 15:28:57 UTC |
| daf32f0 | Gabriel Sanderson | 26 March 2013, 00:06:22 UTC | Merge branch 'master' into gb_master | 26 March 2013, 00:06:22 UTC |
| bf57884 | Gabriel Sanderson | 25 March 2013, 23:58:19 UTC | Clean up many varscan modules. Rely less on samtools_path and more on the pileup_command method. ValidateSmallIndels -add samtools_use_baq flag to pass to varscan validation Add a samtools_path method instead of it being a copypasted param everywhere which was confusing with samtools_version. pileup_command_for_reference_and_bam method now takes an arrayref of bams so it can work for mpileup | 26 March 2013, 00:04:43 UTC |
| cfbd49f | Cyriac Kandoth | 24 March 2013, 20:45:53 UTC | ImportedAnnotation: Support subtracting bps using param flank_size | 24 March 2013, 20:45:53 UTC |
| a330e4c | Gabriel Sanderson | 22 March 2013, 23:26:56 UTC | Merge branch 'nobaq' into gb_master | 22 March 2013, 23:26:56 UTC |
| 5c30788 | Gabriel Sanderson | 22 March 2013, 23:03:33 UTC | DV2 Varscan now recognizes samtools params delimited with : before its own params. There is now the concept of samtools_version, samtools_use_baq, and other samtools params in the varscan base class. | 22 March 2013, 23:14:54 UTC |
| cfc83a3 | Malachi Griffith | 22 March 2013, 22:00:34 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 22 March 2013, 22:00:34 UTC |
| 251a992 | Malachi Griffith | 22 March 2013, 22:00:15 UTC | Blessing clin-seq build to accomodate recent update to cn-view | 22 March 2013, 22:00:15 UTC |
| c6a3706 | nnutter | 22 March 2013, 21:38:00 UTC | more refactoring/testing | 22 March 2013, 21:38:00 UTC |
| 89cb6f6 | dmorton | 22 March 2013, 20:45:06 UTC | Use GENOME_ALIGNER_INDEX_TEST_NAME for chimerascan index instead of GENOME_SOFTWARE_RESULT_TEST_NAME so we can make a test model that doesn't recalculate the index and take forever. | 22 March 2013, 20:45:06 UTC |
| ea2ad9e | dmorton | 22 March 2013, 16:43:27 UTC | ChimerascanVrl behaves just like Chimerascan with reuse-bam=0 with regard to how it gets input fastq files. | 22 March 2013, 19:46:56 UTC |
| 76c7d9d | dmorton | 21 March 2013, 02:30:47 UTC | logic to ChimerascanVrlResult Index to use gtf | 22 March 2013, 19:46:55 UTC |
| d1488b3 | dmorton | 21 March 2013, 16:00:36 UTC | Fix bug about missing version UR::Context->query_underlying_context was called before $self->version and other $self-> lookups forcing UR to look to the data-source for those values, but they haven't been commited at that point. Those lookups are now done before the call. | 22 March 2013, 19:46:55 UTC |
| b1bf4bc | dmorton | 21 March 2013, 19:34:52 UTC | Add *.swp to .gitignore | 22 March 2013, 19:46:55 UTC |
| b1db994 | Chris Miller | 22 March 2013, 19:06:12 UTC | added error logs so that we can go back and see if these bsubbed jobs failed during troubleshooting | 22 March 2013, 19:07:42 UTC |
| bb3229e | Malachi Griffith | 22 March 2013, 18:57:23 UTC | Minor update to cn-view to improve visibilty of copy gains/losses | 22 March 2013, 18:57:23 UTC |
| 33f3fb0 | Dan Koboldt | 22 March 2013, 16:59:43 UTC | Addressing some updates in analysis tools Merge branch 'master' of git+ssh://git/srv/git/genome | 22 March 2013, 16:59:43 UTC |
| c11c83d | Dan Koboldt | 22 March 2013, 16:54:00 UTC | A tool to compute FET p-value expectations based on cases/controls | 22 March 2013, 16:54:00 UTC |
| a187d13 | Dan Koboldt | 22 March 2013, 16:52:59 UTC | New tool for identifying RHRO regions in a VCF | 22 March 2013, 16:52:59 UTC |
| fa3a175 | Dan Koboldt | 22 March 2013, 16:52:33 UTC | Updates to analysis tools | 22 March 2013, 16:52:33 UTC |
| 698dd89 | Dan Koboldt | 22 March 2013, 16:52:20 UTC | Fixed something in refcov reporting | 22 March 2013, 16:52:20 UTC |
| 4593c10 | Dan Koboldt | 22 March 2013, 16:52:02 UTC | Update to Scoring methods | 22 March 2013, 16:52:02 UTC |
| 267f2c5 | Dan Koboldt | 22 March 2013, 16:25:51 UTC | Update to encourage compatibility | 22 March 2013, 16:25:51 UTC |
| c07eade | Malachi Griffith | 22 March 2013, 15:51:30 UTC | Fixed a bug in the display scale for Both_AllChrs.jpeg in cn-view output | 22 March 2013, 15:51:30 UTC |
| dd81eb4 | Jason Walker | 22 March 2013, 14:58:48 UTC | Add the primary_alignment_strategy option to select primary alignment when mutliple alignments are reported per read | 22 March 2013, 14:58:48 UTC |
| 9632873 | Jason Walker | 22 March 2013, 14:57:37 UTC | The param for read_list_file was corrected. | 22 March 2013, 14:57:37 UTC |
| 9c214ce | Jason Walker | 22 March 2013, 14:56:36 UTC | Up the BWASW memory requirement to 16G | 22 March 2013, 14:56:36 UTC |
| 9c7bc7f | nnutter | 22 March 2013, 02:46:10 UTC | add tests for split_dbSNPBuildID | 22 March 2013, 02:53:17 UTC |
| b4382e1 | nnutter | 22 March 2013, 02:45:53 UTC | switch to eval/abort | 22 March 2013, 02:53:16 UTC |
| a4b75e8 | nnutter | 22 March 2013, 02:44:23 UTC | fix uninitialized warning | 22 March 2013, 02:53:16 UTC |
| 3d2140f | nnutter | 22 March 2013, 02:43:52 UTC | add abort | 22 March 2013, 02:53:15 UTC |
| 93e4919 | Gabriel Sanderson | 21 March 2013, 23:18:33 UTC | Merge branch 'master' into gb_master | 21 March 2013, 23:18:33 UTC |
| 1a600f4 | Gabriel Sanderson | 21 March 2013, 23:18:00 UTC | Fixed test data for somatic and somatic-capture models coming back into existence | 21 March 2013, 23:18:28 UTC |
| 5e4b028 | Chris Miller | 21 March 2013, 22:00:41 UTC | bugfix | 21 March 2013, 22:00:48 UTC |
| 087e81f | Gabriel Sanderson | 21 March 2013, 21:36:35 UTC | Merge branch 'varscan' into gb_master | 21 March 2013, 21:36:35 UTC |
| 3be2be0 | Gabriel Sanderson | 21 March 2013, 21:28:29 UTC | Make varscan_validation_version a parameter to PullOneTwoBpIndels. Gather this param from the processing profile of the build | 21 March 2013, 21:36:12 UTC |
| 1bcb1aa | Malachi Griffith | 21 March 2013, 21:29:24 UTC | ClinSeq - update display output in update-analysis and improve figures generated by converge all-events | 21 March 2013, 21:29:24 UTC |
| 291c76a | Eddie Belter | 21 March 2013, 20:03:59 UTC | InstData Solexa: add support for sx trimmer params to have no in the front | 21 March 2013, 20:04:05 UTC |
| fb975bb | Gabriel Sanderson | 21 March 2013, 19:33:30 UTC | Merge branch 'varscan' into gb_master | 21 March 2013, 19:33:30 UTC |
| d38aa27 | Gabriel Sanderson | 21 March 2013, 19:33:20 UTC | Added varscan_validation_version to control varscan version in the validation steps | 21 March 2013, 19:33:20 UTC |
| 2530c3a | Chris Miller | 21 March 2013, 19:16:54 UTC | bsub resource req fix | 21 March 2013, 19:17:06 UTC |
| 59f7ebd | APipe Tester | 21 March 2013, 18:47:50 UTC | updated workflow submodule to 7d78744 | 21 March 2013, 18:47:50 UTC |
| de049aa | nnutter | 21 March 2013, 18:15:35 UTC | Merge branch 'somatic-restore' | 21 March 2013, 18:15:35 UTC |
| cb11c45 | nnutter | 21 March 2013, 18:09:10 UTC | strip down Somatic and SomaticCapture Both have been deprecated and mostly removed. These exist so old models and builds can still be viewed on web and in listers. | 21 March 2013, 18:15:14 UTC |
| 23b5beb | nnutter | 21 March 2013, 17:49:37 UTC | partially restore Somatic and SomaticCapture deletions | 21 March 2013, 18:15:14 UTC |
| 5e874df | Adam Coffman | 21 March 2013, 17:50:48 UTC | increase size of initial allocation request | 21 March 2013, 17:50:48 UTC |
| 56f857d | Eddie Belter | 21 March 2013, 17:31:07 UTC | InstData Import bam: sort before importing; verify paired | 21 March 2013, 17:31:07 UTC |
| 457afc8 | APipe Tester | 21 March 2013, 15:32:55 UTC | updated jenkins submodule to 0d45367 | 21 March 2013, 15:32:55 UTC |
| 9817512 | Kyung Kim | 21 March 2013, 15:23:30 UTC | Added additional functionality params and new versions | 21 March 2013, 15:23:30 UTC |
| 8ee4475 | nnutter | 21 March 2013, 01:43:12 UTC | make test more resilient to GENOME_TEST_INPUTS move After moving GENOME_TEST_INPUTS this test started failing because permissions were not preserved. I made the test actually create the expected filesystem state instead of relying on it from GENOME_TEST_INPUTS. I also corrected an ambiguous test so that there are no two tests; one for each interpretation of the ambiguity. | 21 March 2013, 01:43:12 UTC |
| 422f8d2 | nnutter | 21 March 2013, 00:58:44 UTC | make test more resilient to GENOME_TEST_INPUTS changes | 21 March 2013, 00:58:44 UTC |
| b705b9b | nnutter | 21 March 2013, 00:40:41 UTC | replace test_suite_data path for comparison | 21 March 2013, 00:40:41 UTC |
| dbf2c9a | dmorton | 20 March 2013, 23:17:18 UTC | Fix missing quotes | 20 March 2013, 23:17:18 UTC |
| d3267a9 | dmorton | 20 March 2013, 22:55:45 UTC | Merge branch 'ViewPreview' Adds preview of log files | 20 March 2013, 22:55:45 UTC |
| 936414d | dmorton | 20 March 2013, 22:44:41 UTC | gmb view shows preview of errors or it shows the last line in the error file | 20 March 2013, 22:53:27 UTC |
| 849b052 | dmorton | 20 March 2013, 22:48:17 UTC | Merge branch 'ChimerascanTesting' Fixes tests | 20 March 2013, 22:48:17 UTC |
| e32834c | dmorton | 20 March 2013, 22:40:26 UTC | Add quotes around cmd line args | 20 March 2013, 22:46:40 UTC |
| 07c2840 | dmorton | 20 March 2013, 22:37:25 UTC | Fix test inadvertently testing wrong class | 20 March 2013, 22:46:40 UTC |
| 7423202 | apregier | 20 March 2013, 19:25:56 UTC | Allow dbsnp imports where vcf is split by chromosome | 20 March 2013, 19:26:12 UTC |
| fead616 | Thomas Mooney | 20 March 2013, 14:44:32 UTC | Add picard-tools submodule. | 20 March 2013, 14:44:32 UTC |
| 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 |
