| 328112c | Adam Coffman | 22 October 2013, 22:17:30 UTC | require analysis project in order to sync over from lims | 22 October 2013, 22:17:30 UTC |
| 0b52e9d | Nathan Nutter | 22 October 2013, 22:12:54 UTC | add metric: disk.allocation.create.get_allocation_without_lock.selection | 22 October 2013, 22:12:54 UTC |
| 5a06289 | Nathan Nutter | 22 October 2013, 22:12:28 UTC | add metric: disk.allocation.create.create_directory | 22 October 2013, 22:12:28 UTC |
| a21d471 | Nathan Nutter | 22 October 2013, 22:11:52 UTC | add metric: disk.allocation.create.get_allocation_without_lock | 22 October 2013, 22:11:52 UTC |
| aadbb2a | Nathan Nutter | 22 October 2013, 22:11:30 UTC | add metric: disk.allocation.create.candidate_volumes.existing_allocation_path_check | 22 October 2013, 22:11:30 UTC |
| 2dfb084 | Nathan Nutter | 22 October 2013, 22:10:57 UTC | add metric: disk.allocation.create.candidate_volumes.selection | 22 October 2013, 22:10:57 UTC |
| 6b58d36 | Nathan Nutter | 22 October 2013, 21:52:50 UTC | updated ur submodule to 1af9a22 | 22 October 2013, 21:52:50 UTC |
| c6984b5 | Thomas Mooney | 22 October 2013, 21:35:20 UTC | Add newlines to "native" file output so BED formatter works. | 22 October 2013, 21:35:20 UTC |
| 4afcd23 | Obi Griffith | 22 October 2013, 21:29:39 UTC | modified snv/indel file sources | 22 October 2013, 21:29:39 UTC |
| 37345a6 | APipe Tester | 22 October 2013, 20:44:23 UTC | Updated `genome` tab completion. | 22 October 2013, 20:44:23 UTC |
| 10ea290 | Thomas Mooney | 22 October 2013, 19:48:29 UTC | Corresponding removal of the import expected lines. | 22 October 2013, 19:48:29 UTC |
| 1767dbf | APipe Tester | 22 October 2013, 18:56:12 UTC | Updated `genome` tab completion. | 22 October 2013, 18:56:12 UTC |
| e81e7fc | Malachi Griffith | 22 October 2013, 17:50:14 UTC | clin-seq - add max tumor coverage filter option to generate-clonality-plots command | 22 October 2013, 17:50:14 UTC |
| d97ed08 | Ben Ainscough | 22 October 2013, 14:47:19 UTC | commit | 22 October 2013, 14:47:19 UTC |
| 550a504 | Thomas Mooney | 22 October 2013, 13:25:11 UTC | Test tests live data; live data changes; test fails; expected case updated. Looks like the "format" attribute of these samples was removed. | 22 October 2013, 13:25:11 UTC |
| 19c3866 | APipe Tester | 22 October 2013, 11:19:21 UTC | Updated `genome` tab completion. | 22 October 2013, 11:19:21 UTC |
| a573501 | APipe Tester | 21 October 2013, 19:16:04 UTC | Updated `gmt` tab completion. | 21 October 2013, 19:16:04 UTC |
| 2a0ca78 | APipe Tester | 21 October 2013, 19:15:17 UTC | Updated `genome` tab completion. | 21 October 2013, 19:15:17 UTC |
| 4b9c52b | Nathan Nutter | 21 October 2013, 18:10:53 UTC | use the $DEFAULT_VERSION for the default version | 21 October 2013, 18:11:03 UTC |
| d12686e | Nathan Nutter | 21 October 2013, 18:10:29 UTC | restore default version to 2.3.5 | 21 October 2013, 18:11:02 UTC |
| 735c70d | Nathan Nutter | 21 October 2013, 18:00:02 UTC | whitespace | 21 October 2013, 18:11:02 UTC |
| 2dfd1b7 | Ben Ainscough | 21 October 2013, 17:16:22 UTC | squashed bug that sorted the gene file twice result of git merge error | 21 October 2013, 17:16:22 UTC |
| f40f751 | Ben Ainscough | 21 October 2013, 16:46:32 UTC | fixed tests for MakeCircosPlot.t | 21 October 2013, 16:46:32 UTC |
| 24e3d3b | Ben Ainscough | 21 October 2013, 16:35:29 UTC | Merge branch 'master' of ssh://git/srv/git/genome Conflicts: lib/perl/Genome/Model/ClinSeq/Command/MakeCircosPlot.pm | 21 October 2013, 16:35:29 UTC |
| 510faa0 | Ben Ainscough | 21 October 2013, 14:52:13 UTC | Added a gene list file that includes Amplifications and deletions | 21 October 2013, 14:52:13 UTC |
| dc86ac8 | Thomas Mooney | 21 October 2013, 13:51:32 UTC | Pull out the accessor call--UR carps returning many values in scalar context. | 21 October 2013, 13:51:32 UTC |
| d0c5da3 | Avinash Ramu | 20 October 2013, 02:05:28 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 20 October 2013, 02:05:28 UTC |
| 074b5b0 | Avinash Ramu | 20 October 2013, 02:04:53 UTC | updated all system() calls with Genome::Sys->shellcmd statements for better error logging | 20 October 2013, 02:04:53 UTC |
| 545d0dc | apregier | 18 October 2013, 22:00:29 UTC | Merge branch 'copy' into gb_master | 18 October 2013, 22:00:29 UTC |
| c5cb00d | apregier | 18 October 2013, 21:57:52 UTC | Make output optional | 18 October 2013, 21:57:52 UTC |
| cc4c3a9 | apregier | 18 October 2013, 21:57:17 UTC | If you exclude ensembl annotations, exclude them from the ROI as well | 18 October 2013, 21:57:17 UTC |
| 4e039e6 | apregier | 18 October 2013, 20:53:34 UTC | Find regulatory annotations correctly | 18 October 2013, 20:53:48 UTC |
| a9abcca | Adam Coffman | 18 October 2013, 20:40:23 UTC | only assign a property explicity if it is defined | 18 October 2013, 20:40:23 UTC |
| 3713a25 | apregier | 18 October 2013, 20:02:07 UTC | Add options to ignore ensembl annotations and to not filter on regulomedb | 18 October 2013, 20:02:23 UTC |
| 8ab6973 | APipe Tester | 18 October 2013, 20:01:02 UTC | Updated `genome` tab completion. | 18 October 2013, 20:01:50 UTC |
| ad6e5da | Jason Walker | 18 October 2013, 19:56:57 UTC | Add version 2.3.6 of VarScan | 18 October 2013, 19:56:57 UTC |
| 86aa9d7 | dmorton | 18 October 2013, 19:35:59 UTC | Make tumor-only or normal-only models OK Previously, this tool expected both an experimental_sample and a control_sample, but sometimes we have only one or the other or neither, and this is OK here. | 18 October 2013, 19:37:56 UTC |
| 18298bd | Gabriel Sanderson | 18 October 2013, 19:12:46 UTC | Merge branch 'fpvcf' into gb_master | 18 October 2013, 19:12:46 UTC |
| bbcba69 | Gabriel Sanderson | 18 October 2013, 19:12:30 UTC | Bugfix for the case where we have only one sample name | 18 October 2013, 19:12:40 UTC |
| cdfc8ac | APipe Tester | 18 October 2013, 19:05:45 UTC | Updated `genome` tab completion. | 18 October 2013, 19:05:45 UTC |
| 493ac56 | apregier | 18 October 2013, 18:26:17 UTC | Add some comments | 18 October 2013, 18:26:34 UTC |
| 3521d3a | APipe Tester | 18 October 2013, 18:10:13 UTC | Updated `genome` tab completion. | 18 October 2013, 18:10:13 UTC |
| a6f4557 | Nathan Nutter | 18 October 2013, 17:51:48 UTC | fix typo in BQM lock name | 18 October 2013, 17:52:00 UTC |
| a37c10d | Obi Griffith | 18 October 2013, 16:26:15 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 18 October 2013, 16:26:15 UTC |
| dbf1e54 | Obi Griffith | 18 October 2013, 16:26:00 UTC | modified suggested unarchive command to include lab | 18 October 2013, 16:26:00 UTC |
| ca6ae47 | dmorton | 18 October 2013, 14:57:07 UTC | Revert "Stop using pipefail in PrepareInstrumentData" This reverts commit 00f757aac89cb0a0be05af5777d4ce32d5bcb576. We're now setting the default handler for sigpipe and allowing for exit code 141. See Jira ticket AP-142 for more information. | 18 October 2013, 16:17:08 UTC |
| cce2c4e | apregier | 18 October 2013, 16:11:27 UTC | Allow a base_dir parameter for clinseq test-data | 18 October 2013, 16:11:38 UTC |
| 1649bcc | Nathan Nutter | 17 October 2013, 22:26:44 UTC | Revert "add debug info for the NFS no size issue" This reverts commit b6806470f297b5a35cad7c1b5760d76d81f03ed4. | 18 October 2013, 14:15:53 UTC |
| 0187533 | APipe Tester | 18 October 2013, 11:21:11 UTC | Updated `genome` tab completion. | 18 October 2013, 11:21:11 UTC |
| 8e2ab74 | apregier | 17 October 2013, 22:21:19 UTC | Merge branch 'copy' into gb_master | 17 October 2013, 22:21:19 UTC |
| 55c894e | apregier | 17 October 2013, 22:19:55 UTC | Add data directories for various builds | 17 October 2013, 22:19:55 UTC |
| 6ee65a0 | apregier | 17 October 2013, 22:08:09 UTC | Add optional differential expression model for clinseq test data | 17 October 2013, 22:08:22 UTC |
| 35997a0 | apregier | 17 October 2013, 22:00:36 UTC | Add option to pass in rnaseq models to de test model | 17 October 2013, 22:08:21 UTC |
| 478ce53 | apregier | 17 October 2013, 19:13:44 UTC | Add differential expression test model | 17 October 2013, 22:08:21 UTC |
| 058cf15 | apregier | 17 October 2013, 18:01:59 UTC | Add optional exome model to clinseq test-data | 17 October 2013, 22:08:20 UTC |
| d18e6e0 | apregier | 17 October 2013, 17:45:23 UTC | Add normal rnaseq model to clinseq test-data | 17 October 2013, 22:08:20 UTC |
| 156564e | APipe Tester | 17 October 2013, 22:02:00 UTC | Updated `genome` tab completion. | 17 October 2013, 22:02:00 UTC |
| 03757a4 | APipe Tester | 17 October 2013, 21:56:55 UTC | Updated `genome` tab completion. | 17 October 2013, 21:56:55 UTC |
| 99843a9 | Thomas Mooney | 17 October 2013, 21:46:06 UTC | Just don't worry about the sorting at all for this test. | 17 October 2013, 21:46:06 UTC |
| 5ad48bb | Adam Coffman | 17 October 2013, 21:01:41 UTC | fix aqid tests to look at roi_set_name instead of model name | 17 October 2013, 21:01:41 UTC |
| af27a63 | APipe Tester | 17 October 2013, 20:09:20 UTC | updated jenkins submodule to 603e3e2 | 17 October 2013, 20:09:20 UTC |
| 71e0d53 | Gabriel Sanderson | 17 October 2013, 18:53:04 UTC | Merge branch 'master' into gb_master | 17 October 2013, 18:53:04 UTC |
| 1670072 | Gabriel Sanderson | 17 October 2013, 18:43:05 UTC | do not be confused by -broken symlinks | 17 October 2013, 18:51:56 UTC |
| 4c94733 | Thomas Mooney | 17 October 2013, 18:36:49 UTC | Sort the same way Model sorts--fixes intermittent failures. | 17 October 2013, 18:36:49 UTC |
| d1d3ddb | APipe Tester | 17 October 2013, 18:17:02 UTC | updated ur submodule to 1af9a22 | 17 October 2013, 18:17:02 UTC |
| d82ce87 | Adam Coffman | 17 October 2013, 16:14:57 UTC | respect auto_assign_inst data | 17 October 2013, 16:14:57 UTC |
| 9a09d7c | Adam Coffman | 17 October 2013, 15:53:32 UTC | make CQID utilize auto_assign_inst_data correctly | 17 October 2013, 15:53:32 UTC |
| 3ef1514 | dmorton | 16 October 2013, 20:35:03 UTC | Use build-type agnostic accessors This command should now accept either a somatic-validation or a somatic-validation build as the source_build. | 17 October 2013, 15:40:06 UTC |
| 3576bff | dmorton | 16 October 2013, 20:28:53 UTC | Removed code duplication with delegation | 17 October 2013, 15:40:06 UTC |
| efc99c8 | dmorton | 16 October 2013, 18:13:55 UTC | Added control/experimental_subject to som-var model This is for api-compatibility with somatic-validation models and they have it for APConfig compatiblity. | 17 October 2013, 15:40:06 UTC |
| 8a1e0da | dmorton | 16 October 2013, 17:51:43 UTC | Stop going through tumor_build to get reference_sequence_build This helps make the command compatible for somatic-variation as well as somatic-validation builds. | 17 October 2013, 15:40:06 UTC |
| 0f3a421 | Adam Coffman | 17 October 2013, 15:14:58 UTC | Set correct model names on CQID created models | 17 October 2013, 15:14:58 UTC |
| 0a5689a | APipe Tester | 17 October 2013, 11:18:07 UTC | Updated `genome` tab completion. | 17 October 2013, 11:18:07 UTC |
| 6295019 | APipe Tester | 17 October 2013, 00:19:46 UTC | Updated `genome` tab completion. | 17 October 2013, 00:19:46 UTC |
| 0714820 | Gabriel Sanderson | 16 October 2013, 21:39:26 UTC | Merge branch 'tabix' into gb_master | 16 October 2013, 21:39:26 UTC |
| 1576397 | Gabriel Sanderson | 16 October 2013, 21:22:22 UTC | Clean up unlink_existing_vcf, no longer fail if a greater vcf version exists (which is helpful for testing) | 16 October 2013, 21:39:19 UTC |
| a447d4c | Gabriel Sanderson | 16 October 2013, 20:58:48 UTC | Merge branch 'index' into gb_master | 16 October 2013, 20:58:48 UTC |
| 7115bbc | Gabriel Sanderson | 16 October 2013, 20:58:35 UTC | remove unused output_file property | 16 October 2013, 20:58:35 UTC |
| b680647 | Nathan Nutter | 16 October 2013, 18:48:06 UTC | add debug info for the NFS no size issue This is to help debug INFOSYS-8991. | 16 October 2013, 18:49:57 UTC |
| 4d90b98 | Thomas Mooney | 16 October 2013, 16:11:54 UTC | Add accessor for analysis projects id'd by the analysis_project_id column. | 16 October 2013, 16:11:54 UTC |
| 1c864e7 | APipe Tester | 16 October 2013, 11:18:49 UTC | Updated `genome` tab completion. | 16 October 2013, 11:18:49 UTC |
| 7f866f3 | APipe Tester | 15 October 2013, 20:28:31 UTC | Updated `gmt` tab completion. | 15 October 2013, 20:28:31 UTC |
| d2159ac | APipe Tester | 15 October 2013, 20:27:46 UTC | Updated `genome` tab completion. | 15 October 2013, 20:27:46 UTC |
| c1e10dc | APipe Tester | 15 October 2013, 20:26:02 UTC | Updated class browser cache. | 15 October 2013, 20:26:02 UTC |
| 7f57a75 | Chris Miller | 15 October 2013, 18:04:01 UTC | tool for converting annotation files from one build to another while preserving additional fields | 15 October 2013, 18:08:10 UTC |
| 066f759 | Thomas Mooney | 15 October 2013, 17:50:56 UTC | New simple command to produce a coverage report for a model-group. When the model-group is too big to run via the webserver, this command will (hopefully) be up to the task given enough RAM and patience! | 15 October 2013, 17:50:56 UTC |
| 57f8727 | APipe Tester | 15 October 2013, 15:56:13 UTC | Updated `gmt` tab completion. | 15 October 2013, 15:56:13 UTC |
| 2b3e1c5 | APipe Tester | 15 October 2013, 15:55:29 UTC | Updated `genome` tab completion. | 15 October 2013, 15:55:29 UTC |
| 003728d | Nathan Nutter | 15 October 2013, 15:47:58 UTC | bless new clinseq-wer build with sort changes due to TALC DGIdb datasource | 15 October 2013, 15:47:58 UTC |
| 7ebaeb3 | dmorton | 15 October 2013, 13:51:07 UTC | LongIndelsGenerateMergedAssemblies has annotator_version specified | 15 October 2013, 13:57:57 UTC |
| 2eadf4a | Dave Larson | 14 October 2013, 11:29:32 UTC | add option to summarize only non-assembled indels. Needs to be evaluated. | 15 October 2013, 13:47:34 UTC |
| 6b789ea | APipe Tester | 15 October 2013, 11:48:05 UTC | Updated `genome` tab completion. | 15 October 2013, 11:48:05 UTC |
| 9a1f411 | dmorton | 14 October 2013, 19:09:17 UTC | somatic-validation PPs have annotator-version I've also backfilled the database to specify 2 for all existing processing-profiles, as this reflects what the default was up until now. | 14 October 2013, 19:09:17 UTC |
| 0548035 | APipe Tester | 14 October 2013, 11:18:39 UTC | Updated `genome` tab completion. | 14 October 2013, 11:18:39 UTC |
| ae4106e | APipe Tester | 13 October 2013, 11:19:00 UTC | Updated `genome` tab completion. | 13 October 2013, 11:19:00 UTC |
| e1f5b28 | APipe Tester | 12 October 2013, 12:13:09 UTC | Updated `gmt` tab completion. | 12 October 2013, 12:13:09 UTC |
| 7fc6893 | APipe Tester | 12 October 2013, 12:12:18 UTC | Updated `genome` tab completion. | 12 October 2013, 12:12:18 UTC |
| 36c867a | APipe Tester | 12 October 2013, 12:10:32 UTC | Updated class browser cache. | 12 October 2013, 12:10:32 UTC |
| 8d843fb | dmorton | 11 October 2013, 23:17:09 UTC | Extract function for removing ids and paths And use it for both Failed and Unstartable | 11 October 2013, 23:17:09 UTC |
| e7a89e8 | dmorton | 11 October 2013, 23:15:48 UTC | Updated test data for g m import metadata This test should really stop depending on the output of g m export metadata's test data | 11 October 2013, 23:15:48 UTC |
