| e78395d | Dave Larson | 14 September 2015, 15:09:32 UTC | Merge pull request #985 from ernfrid/gold_report Gold report | 14 September 2015, 15:09:32 UTC |
| 2c8bde9 | Thomas B. Mooney | 14 September 2015, 13:26:50 UTC | Merge pull request #994 from tmooney/analysis_id_and_seq_id_are_different Return analysis ID but join on seq ID. | 14 September 2015, 13:26:50 UTC |
| a5fc777 | Thomas B. Mooney | 14 September 2015, 13:20:01 UTC | Merge pull request #993 from tmooney/cqid_processes_data_batched_by_sample CQID processes data batched by sample | 14 September 2015, 13:20:01 UTC |
| 31db617 | Jason Walker | 11 September 2015, 14:55:11 UTC | Merge pull request #992 from jasonwalker80/another_annotation_user Add another users hash to the annotation result get_or_create | 11 September 2015, 14:55:11 UTC |
| a1a120c | Feiyu Du | 10 September 2015, 20:42:32 UTC | Merge pull request #989 from dufeiyu/superseding New method get_superseding_results added to Merged.pm | 10 September 2015, 20:42:32 UTC |
| 52bfd5d | Thomas Mooney | 10 September 2015, 18:08:26 UTC | A pure-UR version of deciding what samples to process. This will pick a sample based on the minimum of its fail count instead of the total, but should still allow progress on non-failing samples in the presence of failures. | 10 September 2015, 18:08:26 UTC |
| d19659d | Thomas Mooney | 10 September 2015, 17:52:41 UTC | Return analysis ID but join on seq ID. The "analysis ID" is only used to map to the Genome object. Everywhere else the "seq ID" is used to refer to the object within the LIMS schema. | 10 September 2015, 17:52:41 UTC |
| 051791f | Jason Walker | 10 September 2015, 15:06:41 UTC | Add another users hash to the annotation result get_or_create | 10 September 2015, 15:06:41 UTC |
| 071f62e | Thomas Mooney | 10 September 2015, 14:54:16 UTC | Fill in the other string that sprintf is expecting. | 10 September 2015, 15:03:36 UTC |
| 6cd7580 | Thomas Mooney | 10 September 2015, 14:52:48 UTC | Batch instrument data by sample. This will reduce the number of "partial" builds that get launched before being nearly immediately superseded. | 10 September 2015, 15:03:36 UTC |
| a1918d5 | Jason Walker | 10 September 2015, 15:02:59 UTC | Merge pull request #991 from tmooney/users_not_user_data Use the correct key for passing users. | 10 September 2015, 15:02:59 UTC |
| 46fa601 | Dave Larson | 10 September 2015, 13:40:51 UTC | add back same_file: 0 line | 10 September 2015, 13:40:51 UTC |
| 52df5cc | APipe Tester | 10 September 2015, 12:18:33 UTC | Updated `gmt` tab completion. | 10 September 2015, 12:18:33 UTC |
| 0a25a10 | APipe Tester | 10 September 2015, 12:17:38 UTC | Updated `genome` tab completion. | 10 September 2015, 12:17:38 UTC |
| 9f6c98b | Chris Miller | 09 September 2015, 18:46:27 UTC | Merge pull request #990 from chrisamiller/binding new options for epitope binding filter | 09 September 2015, 18:46:27 UTC |
| 921a766 | Feiyu Du | 09 September 2015, 18:07:01 UTC | Merge pull request #988 from dufeiyu/orphan Make FixOrphanedAllocationsForDv2Results run on multiple builds | 09 September 2015, 18:07:01 UTC |
| a42a4a1 | Feiyu Du | 09 September 2015, 16:11:40 UTC | change variable names | 09 September 2015, 16:11:40 UTC |
| 8cefcc1 | Feiyu Du | 09 September 2015, 15:53:04 UTC | remove if/else block | 09 September 2015, 15:53:04 UTC |
| e160088 | Chris Miller | 09 September 2015, 15:42:36 UTC | cleaning up file handlers (thanks dlarson) | 09 September 2015, 15:42:36 UTC |
| bd7e4cf | Thomas Mooney | 09 September 2015, 15:25:56 UTC | Use the correct key for passing users. | 09 September 2015, 15:25:56 UTC |
| fe9db0c | Chris Miller | 08 September 2015, 20:53:21 UTC | new options for epitope binding filter | 08 September 2015, 20:53:21 UTC |
| 5bc7569 | Feiyu Du | 08 September 2015, 16:12:53 UTC | update unit test | 08 September 2015, 16:12:53 UTC |
| f796091 | Feiyu Du | 08 September 2015, 16:12:13 UTC | add new method get_superseding_results to Merged.pm | 08 September 2015, 16:12:13 UTC |
| a232a13 | Feiyu Du | 03 September 2015, 20:34:08 UTC | Make it run on multiple builds | 03 September 2015, 20:34:08 UTC |
| 948c788 | Jason Walker | 03 September 2015, 17:29:03 UTC | Merge pull request #986 from tmooney/pass_build_to_tiering_construction Pass build to tiering command so user info is available. | 03 September 2015, 17:29:03 UTC |
| 9a80926 | Feiyu Du | 03 September 2015, 17:27:40 UTC | Merge pull request #978 from dufeiyu/ldap Iterate through ldapsearch output | 03 September 2015, 17:27:40 UTC |
| af5d065 | Jason Walker | 03 September 2015, 17:23:57 UTC | Merge pull request #959 from obigriffith/master added new hard-coded path for mm10 tiering files | 03 September 2015, 17:23:57 UTC |
| cd66f8b | Jason Walker | 03 September 2015, 17:20:36 UTC | Merge pull request #963 from jasonwalker80/mouse_annotation_structures Add new annotation structures found in mouse 79_38 import. | 03 September 2015, 17:20:36 UTC |
| b775dee | Eddie Belter | 03 September 2015, 16:57:04 UTC | Merge pull request #987 from gatoravi/ignore_dgidb_diffs Ignore DGIdb interaction files in the clinseq build-test | 03 September 2015, 16:57:04 UTC |
| a597e96 | Anthony Brummett | 03 September 2015, 15:42:16 UTC | Merge pull request #984 from brummett/remove-test-allocations Remove newly created disk allocations when exiting genome-env | 03 September 2015, 15:42:16 UTC |
| a3ac962 | APipe Tester | 03 September 2015, 12:18:57 UTC | Updated `gmt` tab completion. | 03 September 2015, 12:18:57 UTC |
| 72de62b | APipe Tester | 03 September 2015, 12:18:08 UTC | Updated `genome` tab completion. | 03 September 2015, 12:18:08 UTC |
| 59eb6aa | APipe Tester | 03 September 2015, 12:16:29 UTC | Updated class browser cache. | 03 September 2015, 12:16:29 UTC |
| 879291d | Avinash Ramu | 02 September 2015, 21:55:48 UTC | Add dgidb files to list of diff-ignored files | 02 September 2015, 21:55:48 UTC |
| 09fd7e6 | Thomas Mooney | 02 September 2015, 17:36:28 UTC | Pass build to tiering command so user info is available. | 02 September 2015, 17:36:28 UTC |
| b5b20c0 | Thomas B. Mooney | 02 September 2015, 17:17:30 UTC | Merge pull request #960 from tmooney/cleanup_succeeded_ignores_abandoned CleanupSucceeded considers the status of the newest non-abandoned build. | 02 September 2015, 17:17:30 UTC |
| fa635e9 | Thomas B. Mooney | 02 September 2015, 16:04:55 UTC | Merge pull request #941 from tmooney/add_gatk_haplotype_caller Add `gmt` tool for GATK HaplotypeCaller | 02 September 2015, 16:04:55 UTC |
| 6515b8a | Jim Eldred | 02 September 2015, 15:10:52 UTC | Merge pull request #962 from jasonwalker80/override_microarray_sample Optional microarray build for Picard GenotypeConcordance | 02 September 2015, 15:10:52 UTC |
| e00bf33 | Dave Larson | 02 September 2015, 14:24:29 UTC | Clean up gold somatic reports + remove homopolymer filter from gold indel report plans + remove extraneous reports and drop min coverage filter | 02 September 2015, 14:24:29 UTC |
| 4087add | Dave Larson | 02 September 2015, 14:21:35 UTC | Clean up the germline gold report + remove homopolymer filter from gold indel report plans + remove extraneous reports and drop min coverage filter + remove extraneous reports and drop min coverage filter + include 'reference_version' and 'allow_same_file' | 02 September 2015, 14:21:35 UTC |
| 330dc15 | Thomas B. Mooney | 02 September 2015, 13:28:33 UTC | Merge pull request #976 from davidlmorton/ptero_job Update how ptero workflows are constructed | 02 September 2015, 13:28:33 UTC |
| f93a1b5 | Thomas B. Mooney | 02 September 2015, 13:07:39 UTC | Merge pull request #961 from tmooney/use_config_for_queue_selection Add configurable LSF queues to many pipelined commands | 02 September 2015, 13:07:39 UTC |
| 2fa38b4 | Thomas B. Mooney | 02 September 2015, 13:05:58 UTC | Merge pull request #966 from tmooney/db_ensembl_annotationstructures_unlocks_once Only unlock SoftwareResults once. | 02 September 2015, 13:05:58 UTC |
| 0d42e97 | Thomas B. Mooney | 02 September 2015, 13:05:22 UTC | Merge pull request #977 from tmooney/required_users_for_tier_bitmasks Add required-users for fast-tier bitmask generation. | 02 September 2015, 13:05:22 UTC |
| abe1b4e | APipe Tester | 02 September 2015, 12:18:54 UTC | Updated `genome` tab completion. | 02 September 2015, 12:18:54 UTC |
| 4374c9e | APipe Tester | 02 September 2015, 12:16:59 UTC | Updated class browser cache. | 02 September 2015, 12:16:59 UTC |
| b418b3b | Eddie Belter | 01 September 2015, 22:21:14 UTC | Merge pull request #964 from ebelter/ref-cov-metrics-non-succ-builds Ref Cov Metrics Command | 01 September 2015, 22:21:14 UTC |
| b87f6aa | Eddie Belter | 01 September 2015, 21:06:23 UTC | Merge pull request #953 from ebelter/dv2-lsf-resource-config DV2: Use config to get lsf resources | 01 September 2015, 21:06:23 UTC |
| 9e9dd01 | Anthony Brummett | 01 September 2015, 20:36:18 UTC | Remove newly created disk allocations when exiting genome-env Before the test database is deleted, remove any allocations created during this invocation of genome-env | 01 September 2015, 20:39:05 UTC |
| 916c68e | Anthony Brummett | 01 September 2015, 20:27:33 UTC | Merge pull request #932 from brummett/allocations-in-test-db Remove allocations in test db | 01 September 2015, 20:27:33 UTC |
| b625fbc | Thomas B. Mooney | 01 September 2015, 20:26:02 UTC | Merge pull request #980 from tmooney/update_dgidb_test_to_v4 Update test to account for new DGIdb release. | 01 September 2015, 20:26:02 UTC |
| a4fd3bf | Thomas Mooney | 01 September 2015, 19:58:02 UTC | Stop comparing to an expected file since results will change. | 01 September 2015, 19:58:02 UTC |
| 82c98a9 | Feiyu Du | 01 September 2015, 19:08:03 UTC | use Genome::Config::get email_domain | 01 September 2015, 19:08:03 UTC |
| c934962 | Susanna Siebert | 01 September 2015, 18:50:49 UTC | Merge pull request #981 from susannasiebert/speedseq_memory Increase speedseq LSF memory requested | 01 September 2015, 18:50:49 UTC |
| f86315d | Feiyu Du | 01 September 2015, 18:25:49 UTC | add unit test | 01 September 2015, 18:25:49 UTC |
| 84cf049 | Feiyu Du | 01 September 2015, 18:25:05 UTC | use command pipe to iterate through idapsearch output | 01 September 2015, 18:25:05 UTC |
| 938e610 | Thomas B. Mooney | 01 September 2015, 18:23:43 UTC | Merge pull request #982 from tmooney/update_cle_test_to_match_updated_blessed_process Update CLE test to match updated blessed process. | 01 September 2015, 18:23:43 UTC |
| 832fd10 | Thomas Mooney | 01 September 2015, 18:01:12 UTC | Update test to match updated blessed process in #965. | 01 September 2015, 18:01:12 UTC |
| 8971b7b | Susanna Siebert | 01 September 2015, 17:58:24 UTC | Increase speedseq LSF memory requested since 36G is not enough for some large instrument data | 01 September 2015, 17:58:24 UTC |
| 60bff44 | Thomas Mooney | 01 September 2015, 17:38:50 UTC | Update test to account for new DGIdb release. | 01 September 2015, 17:38:50 UTC |
| cdab672 | Adam Coffman | 01 September 2015, 17:28:52 UTC | Merge pull request #979 from acoffman/bwa_version_for_speedseq_010 Add entry for speedseq version to bwa version mapping | 01 September 2015, 17:28:52 UTC |
| a63a967 | Adam Coffman | 01 September 2015, 17:12:23 UTC | add test to ensure future speedseq to bwa mappings are added | 01 September 2015, 17:12:23 UTC |
| cd48327 | Jason Walker | 01 September 2015, 16:46:59 UTC | New name for boolean to lookup lane QC builds. | 01 September 2015, 16:46:59 UTC |
| 135b4a1 | Allison Penner Regier | 01 September 2015, 15:43:30 UTC | Merge pull request #965 from apregier/update_blessed_process Update CLE Test | 01 September 2015, 15:43:30 UTC |
| 506adbc | Adam Coffman | 01 September 2015, 15:37:27 UTC | add entry for speedseq version to bwa mapping | 01 September 2015, 15:37:27 UTC |
| e0e231b | Feiyu Du | 01 September 2015, 15:33:56 UTC | remove the size limit of response for ldapsearch | 01 September 2015, 15:33:56 UTC |
| c36c338 | Jason Walker | 01 September 2015, 15:15:24 UTC | Merge pull request #974 from jasonwalker80/basic_qc_report Basic refalign QC summary. | 01 September 2015, 15:15:24 UTC |
| c92a757 | Thomas B. Mooney | 01 September 2015, 12:54:19 UTC | Merge pull request #975 from genome/revert-969-loh_write_to_tempdir Revert "ClinSeq::LOH - Write results to temp dir first." | 01 September 2015, 12:54:19 UTC |
| ef424ba | Thomas Mooney | 31 August 2015, 22:27:58 UTC | Add required-users for fast-tier bitmask generation. | 31 August 2015, 22:27:58 UTC |
| 487a541 | dmorton | 31 August 2015, 20:07:07 UTC | Update how ptero workflows are constructed Ptero::Builder::ShellCommand has been generalized to Ptero::Builder::Job, but it requires a service_url to be specified. | 31 August 2015, 21:02:47 UTC |
| 19c9349 | Jason Walker | 31 August 2015, 16:55:06 UTC | A few corrections from code review. Mainly use the input microarray_build property to determine if a builds microarray data is to be used. | 31 August 2015, 16:55:06 UTC |
| 99700ee | Anthony Brummett | 31 August 2015, 16:27:56 UTC | Use the Genome::Config API to get the env variable names instead of leaving them hard-coded | 31 August 2015, 16:27:56 UTC |
| ef7be06 | Thomas B. Mooney | 31 August 2015, 14:54:22 UTC | Revert "ClinSeq::LOH - Write results to temp dir first." | 31 August 2015, 14:54:22 UTC |
| e14d5cb | Jason Walker | 31 August 2015, 14:08:26 UTC | Add the removal of AdspQcSummary that was missed in last commit. | 31 August 2015, 14:08:26 UTC |
| 77c629a | APipe Tester | 29 August 2015, 12:18:45 UTC | Updated `genome` tab completion. | 29 August 2015, 12:18:45 UTC |
| 2fc0bf3 | APipe Tester | 29 August 2015, 12:16:56 UTC | Updated class browser cache. | 29 August 2015, 12:16:56 UTC |
| c48f5a6 | Eddie Belter | 28 August 2015, 23:06:26 UTC | DV2 LSF resource Config: add XGENOME envs | 28 August 2015, 23:06:26 UTC |
| b264274 | Avinash Ramu | 28 August 2015, 20:17:18 UTC | Merge pull request #969 from gatoravi/loh_write_to_tempdir ClinSeq::LOH - Write results to temp dir first. | 28 August 2015, 20:17:18 UTC |
| 6695579 | Jason Walker | 28 August 2015, 19:41:46 UTC | Remove the ADSP QC command and make it applicable to all projects. | 28 August 2015, 19:41:46 UTC |
| b591225 | Feiyu Du | 28 August 2015, 18:56:48 UTC | Merge pull request #972 from dufeiyu/test_fix Update GetBamReadCountsMatrix.t with the new som-var build | 28 August 2015, 18:56:48 UTC |
| eab2ce0 | Allison Penner Regier | 28 August 2015, 18:30:50 UTC | Merge pull request #967 from apregier/add_filldb_script Script to set up the fill_db environment in which you can pull in obj… | 28 August 2015, 18:30:50 UTC |
| 70a5387 | Feiyu Du | 28 August 2015, 18:03:31 UTC | update test DB | 28 August 2015, 18:03:31 UTC |
| 96aa113 | Feiyu Du | 28 August 2015, 17:59:58 UTC | update this test with new som-var build | 28 August 2015, 17:59:58 UTC |
| 694b352 | Eddie Belter | 27 August 2015, 21:21:36 UTC | Merge pull request #939 from ebelter/bam-readcount-version Handle insert_centric Option for Bam Readcount | 27 August 2015, 21:21:36 UTC |
| b641b21 | apregier | 27 August 2015, 20:29:39 UTC | Update error message | 27 August 2015, 20:29:39 UTC |
| 4042947 | Avinash Ramu | 27 August 2015, 20:13:19 UTC | Remove stray variable | 27 August 2015, 20:13:19 UTC |
| 1dfda5b | Feiyu Du | 27 August 2015, 19:55:52 UTC | Merge pull request #968 from dufeiyu/laneqc Update lane qc blessed build in DiffBlessed.pm.YAML | 27 August 2015, 19:55:52 UTC |
| 3e99270 | Avinash Ramu | 27 August 2015, 19:12:20 UTC | Write results to temp dir This PR modifies this module to write the results to a temp dir and copy results over at the end for better performance. | 27 August 2015, 19:12:20 UTC |
| a6be65e | Thomas B. Mooney | 27 August 2015, 18:18:55 UTC | Merge pull request #912 from tmooney/disabled_configs_imply_disabled_models Disabled configs imply disabled models CHANGELOG: If a configuration for an Analysis Project has been disabled, models created from that configuration will now report their status as "Disabled". | 27 August 2015, 18:18:55 UTC |
| 3d1aca8 | Feiyu Du | 27 August 2015, 18:14:23 UTC | update lane qc blessed build | 27 August 2015, 18:14:23 UTC |
| 70c406e | apregier | 27 August 2015, 17:41:12 UTC | Script to set up the fill_db environment in which you can pull in objects from the production db into a test db | 27 August 2015, 17:41:12 UTC |
| 53b566f | David Morton | 27 August 2015, 17:38:06 UTC | Merge pull request #931 from davidlmorton/ptero_optional_inputproperties Ptero runs workflows with optional inputproperties | 27 August 2015, 17:38:06 UTC |
| 0e56556 | Thomas B. Mooney | 27 August 2015, 16:11:37 UTC | Merge pull request #914 from tmooney/model_summary_wont_retry_memlimit_failures Don't auto-retry MEMLIMIT errors and orphaned allocations. | 27 August 2015, 16:11:37 UTC |
| f9897d4 | Adam Coffman | 27 August 2015, 16:05:43 UTC | Merge pull request #881 from rfugina/dont_do_extra_work Don't do extra work that we're just going to throw away | 27 August 2015, 16:05:43 UTC |
| 77c2bd3 | Thomas Mooney | 27 August 2015, 15:10:07 UTC | Can't rely on a commit observer to unlock when we commit midstream. Instead add an explicit unlock after our last commit(). | 27 August 2015, 15:10:07 UTC |
| 2fbd3ba | Thomas Mooney | 27 August 2015, 15:09:39 UTC | Extract subroutine for creating observers (so we can override it). | 27 August 2015, 15:09:39 UTC |
| ea3f418 | Thomas Mooney | 27 August 2015, 14:27:35 UTC | If the user gave us a test name, use it. | 27 August 2015, 14:27:35 UTC |
| 4f5d67a | Thomas Mooney | 27 August 2015, 14:26:25 UTC | Only try to unlock once! | 27 August 2015, 14:26:25 UTC |
| 4b2d3db | apregier | 26 August 2015, 21:55:04 UTC | Update blessed process for CLE test | 26 August 2015, 21:55:04 UTC |
| c78fdc9 | Eddie Belter | 26 August 2015, 19:15:59 UTC | Remove accidental addition! | 26 August 2015, 19:15:59 UTC |
