| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 152b0b8 | Eddie Belter | 26 August 2015, 19:10:39 UTC | GMT Analysis Cov Bam RC Revert checking to see if bam read count version supports insertion_centric in the gmt analysis cov bam. This will get passed to the gmt bam read count and ultimately fail. This is required at this time to catch the instances of bam read count v0.4 being used in this process. This reverts commit 551627d2f81c17d56ecd77981fb09dcb30cc8c60. | 26 August 2015, 19:10:53 UTC |
| 039ec9f | Eddie Belter | 26 August 2015, 18:49:32 UTC | Ref Cov Metrics Cmd: order by created_at | 26 August 2015, 18:49:32 UTC |
| f32662b | Eddie Belter | 26 August 2015, 18:07:45 UTC | Ref Cov Metrics Command add param to inlcude non succeeded builds sort by date_scheduled | 26 August 2015, 18:07:45 UTC |
| 7d55040 | Jason Walker | 26 August 2015, 17:14:56 UTC | Add options to over-ride the microarray data used. Limit the concordance for Exome analysis to the ROI. Utilize gzipped and indexed VCF whenever possible. | 26 August 2015, 17:14:56 UTC |
| 609911c | Thomas B. Mooney | 26 August 2015, 15:51:15 UTC | Merge pull request #958 from tmooney/skip_small_indel_validation_if_no_small_indels Skip running the small indel workflow if there aren't any small indels. | 26 August 2015, 15:51:15 UTC |
| 70481ff | Thomas Mooney | 26 August 2015, 15:15:32 UTC | Add lsf queue to somval's review variants. | 26 August 2015, 15:15:32 UTC |
| c5a3e50 | Thomas Mooney | 26 August 2015, 15:11:12 UTC | Add lsf queue to BamQC steps. | 26 August 2015, 15:11:12 UTC |
| 85e489e | Thomas Mooney | 26 August 2015, 14:51:02 UTC | Add LSF queue specification to coverage stats summaries. | 26 August 2015, 14:55:02 UTC |
| fbe2497 | Thomas Mooney | 26 August 2015, 14:46:21 UTC | Specify LSF Queues for fusion detection steps. | 26 August 2015, 14:55:01 UTC |
| 14d17b3 | Jason Walker | 26 August 2015, 14:36:09 UTC | Merge pull request #954 from jasonwalker80/more_new_annotation_structures More annotation structure updates to biotype map. | 26 August 2015, 14:36:09 UTC |
| 197410b | Thomas Mooney | 25 August 2015, 17:19:40 UTC | Skip running the small indel workflow if there aren't any small indels. | 25 August 2015, 17:19:40 UTC |
| 7432dcd | Jason Walker | 25 August 2015, 17:11:03 UTC | alphabetical order ncrna list | 25 August 2015, 17:11:03 UTC |
| f137fd5 | Adam Coffman | 25 August 2015, 15:28:17 UTC | Merge pull request #950 from acoffman/add_new_speedseq_freeze Add path for 0.1.0 freeze of speedseq gms branch | 25 August 2015, 15:28:17 UTC |
| cb877d9 | Adam Coffman | 24 August 2015, 20:13:55 UTC | update expected output VCF with new version | 24 August 2015, 22:33:12 UTC |
| 7dd7ef6 | Anthony Brummett | 24 August 2015, 22:00:05 UTC | remove unused function | 24 August 2015, 22:00:05 UTC |
| 7dcf704 | Anthony Brummett | 24 August 2015, 21:16:52 UTC | For new allocations, check to see if it's in the production DB Some testing situations want to copy production allocation info into the test DB that didn't exist in the template. Don't delete allocations that appear in production. | 24 August 2015, 21:16:52 UTC |
| 669537e | Anthony Brummett | 24 August 2015, 20:56:30 UTC | only need to get the server setting once | 24 August 2015, 20:56:30 UTC |
| 64bb8aa | Anthony Brummett | 24 August 2015, 20:55:54 UTC | Rename method - We're not using env vars any more | 24 August 2015, 20:55:54 UTC |
| 54144a3 | Anthony Brummett | 24 August 2015, 20:39:01 UTC | Change detection for running in test env It now asks the test DB server whether the current database settings refer to a known test DB. Test databases are used not only when running in genome-test-env, but also genome-env | 24 August 2015, 20:40:32 UTC |
| 0b7b8ba | Thomas Mooney | 24 August 2015, 17:38:35 UTC | Add an option for GVCF GQ bands. | 24 August 2015, 17:40:46 UTC |
| 96a25a2 | Thomas B. Mooney | 24 August 2015, 14:34:33 UTC | Merge pull request #926 from tmooney/build_output_properties Lend functionality to "is_output" build properties. | 24 August 2015, 14:34:33 UTC |
| 04a6b72 | Thomas B. Mooney | 24 August 2015, 13:29:31 UTC | Merge pull request #949 from tmooney/qc_buildmetrics_extract_subroutine Extract metrics_for_build subroutine for programmatic convenience. | 24 August 2015, 13:29:31 UTC |
| 0dac42b | Thomas Mooney | 24 August 2015, 13:20:54 UTC | Revert "Get test passing for new version of GATK" This reverts commit 09838d68b7845b55516e63823ece272599dc4661. | 24 August 2015, 13:20:54 UTC |
| 4432504 | Thomas Mooney | 19 August 2015, 15:46:22 UTC | Fix bug in Sys-sw.t | 24 August 2015, 13:20:37 UTC |
| 957caa0 | Thomas Mooney | 18 August 2015, 18:58:27 UTC | Add gmt wrapper for GATK HaplotypeCaller. | 24 August 2015, 13:20:37 UTC |
| cf0645b | Thomas Mooney | 18 August 2015, 18:07:17 UTC | Provide a way to configure alternate Java installations. | 24 August 2015, 13:20:37 UTC |
| 6753ab0 | Thomas Mooney | 18 August 2015, 13:22:43 UTC | Add 3.4 as an installed GATK version. | 24 August 2015, 13:20:37 UTC |
| bbc0ed0 | Thomas Mooney | 17 August 2015, 18:28:00 UTC | Allow the java interpreter to be customized. | 24 August 2015, 13:20:37 UTC |
| 7b58453 | Jason Walker | 21 August 2015, 21:56:13 UTC | Add translated_unprocessed_pseudogene from PR951 to this PR to avoid merge conflict. | 21 August 2015, 21:56:13 UTC |
| 5574d46 | Jason Walker | 21 August 2015, 21:53:33 UTC | Merge pull request #955 from genome/revert-951-new_annotation_structure Revert "translated_unprocessed_pseudogene added to AnnotationStructures" | 21 August 2015, 21:53:33 UTC |
| 0172ca1 | Jason Walker | 21 August 2015, 21:53:16 UTC | Revert "translated_unprocessed_pseudogene added to AnnotationStructures" | 21 August 2015, 21:53:16 UTC |
| a38d6a9 | Jason Walker | 21 August 2015, 21:52:03 UTC | Merge pull request #951 from jasonwalker80/new_annotation_structure translated_unprocessed_pseudogene added to AnnotationStructures | 21 August 2015, 21:52:03 UTC |
| 485ef1c | Jason Walker | 21 August 2015, 21:46:18 UTC | Several new gene biotypes added to the AnnotationStructures biotype class map. | 21 August 2015, 21:46:18 UTC |
| f07e342 | Eddie Belter | 21 August 2015, 21:15:59 UTC | Merge pull request #935 from ebelter/update-rm CRUD: remove unused update class | 21 August 2015, 21:15:59 UTC |
| 1a28db0 | Eddie Belter | 21 August 2015, 20:56:03 UTC | DV2: classes use config to get lsf resource | 21 August 2015, 20:56:03 UTC |
| ad7a012 | Anthony Brummett | 21 August 2015, 19:32:34 UTC | Merge pull request #952 from brummett/gatk-test Get test passing for new version of GATK | 21 August 2015, 19:32:34 UTC |
| 09838d6 | Anthony Brummett | 21 August 2015, 18:45:39 UTC | Get test passing for new version of GATK | 21 August 2015, 18:45:39 UTC |
| 577a22a | Allison Penner Regier | 21 August 2015, 18:37:03 UTC | Merge pull request #948 from apregier/handle_error_rate Handle error rate | 21 August 2015, 18:37:03 UTC |
| e787729 | apregier | 21 August 2015, 18:00:46 UTC | Add (minimal) test for alignment stats summary This test case failed before my fix to the error rate, and it now passes. (Before it showed 0.00 and now it shows NA) | 21 August 2015, 18:00:46 UTC |
| d661154 | Allison Penner Regier | 21 August 2015, 16:51:50 UTC | Merge pull request #947 from apregier/trio_process_fixes Trio process fixes | 21 August 2015, 16:51:50 UTC |
| 6c94c20 | Jason Walker | 21 August 2015, 16:33:12 UTC | Merge pull request #945 from tmooney/add_required_users_for_ensembl_annotation_structures Add required-users for annotation structure importer. | 21 August 2015, 16:33:12 UTC |
| 8464063 | Jason Walker | 21 August 2015, 16:30:51 UTC | Merge pull request #946 from tmooney/add_scarna_ensembl_biotype Add scaRNA as a non-coding RNA biotype. | 21 August 2015, 16:30:51 UTC |
| 9923d8a | Jason Walker | 21 August 2015, 16:17:31 UTC | Add translated_unprocessed_pseudogene to the list of coding_pseudogene biotype classes | 21 August 2015, 16:17:31 UTC |
