| 1621125 | Thomas B. Mooney | 03 August 2015, 21:01:08 UTC | Merge pull request #896 from tmooney/indices_set_archivable_false Primary References and Indices Default to Not Archivable | 03 August 2015, 21:01:08 UTC |
| 029abd6 | Thomas B. Mooney | 03 August 2015, 15:36:22 UTC | Merge pull request #891 from tmooney/tolerate_unused_annotation_input Only schedule annotation if we have variants to annotate. | 03 August 2015, 15:36:22 UTC |
| 1c9330c | Thomas Mooney | 30 July 2015, 20:11:10 UTC | Prevent archiving of basic data. Typically these allocations are too small to archive, anyway! | 03 August 2015, 15:30:22 UTC |
| 2bb803e | Thomas Mooney | 30 July 2015, 19:56:00 UTC | Don't allow archiving of main indices. (Indices for "rederivable" references are not widely used and so can generally still be archived.) | 03 August 2015, 15:30:22 UTC |
| ce51605 | Allison Penner Regier | 03 August 2015, 15:20:10 UTC | Merge pull request #897 from apregier/build_diff_change Don't require builds to be from the same model to diff | 03 August 2015, 15:20:10 UTC |
| 8291dee | apregier | 31 July 2015, 17:10:57 UTC | Don't require builds to be from the same model to diff We have a use case for CLE regression testing where we are making new models in a testdb and want to diff the resulting builds with builds from old models. They should be equivalent, but not the same model. I don't see any reason why this check adds to the integrity of the diff | 31 July 2015, 17:13:27 UTC |
| f941263 | Thomas B. Mooney | 30 July 2015, 18:50:54 UTC | Merge pull request #893 from tmooney/somvar_loh_requires_normal_snv_detection Don't try to run LOH without a normal to compare to. | 30 July 2015, 18:50:54 UTC |
| 21ac56c | APipe Tester | 30 July 2015, 12:19:39 UTC | Updated `gmt` tab completion. | 30 July 2015, 12:19:39 UTC |
| f9d4e66 | APipe Tester | 30 July 2015, 12:18:46 UTC | Updated `genome` tab completion. | 30 July 2015, 12:18:46 UTC |
| 27025fe | Eddie Belter | 29 July 2015, 20:46:15 UTC | Merge pull request #886 from ebelter/gm-cc GM Concordance | 29 July 2015, 20:46:15 UTC |
| cc80ae5 | Thomas Mooney | 29 July 2015, 17:01:19 UTC | Check the model instead of the build. (Some build types don't provide direct access to the PP params.) | 29 July 2015, 17:48:41 UTC |
| b857579 | Thomas B. Mooney | 29 July 2015, 15:34:21 UTC | Merge pull request #880 from tmooney/dump_flagstats_on_error Dump flagstat data when comparison fails. | 29 July 2015, 15:34:21 UTC |
| b46679b | Thomas B. Mooney | 29 July 2015, 15:33:54 UTC | Merge pull request #892 from tmooney/cleanup_sync_sys_user_with_ldap LDAP Synch: Fix counting bug and cleanup | 29 July 2015, 15:33:54 UTC |
| b6cb0e5 | Allison Penner Regier | 29 July 2015, 15:32:37 UTC | Merge pull request #887 from apregier/bedpe Add the ability to specify a minimum number of hits required | 29 July 2015, 15:32:37 UTC |
| 52ca980 | Thomas Mooney | 29 July 2015, 13:43:38 UTC | Don't try to run LOH without a normal to compare to. | 29 July 2015, 14:14:59 UTC |
| cf0c7b8 | APipe Tester | 29 July 2015, 12:19:21 UTC | Updated `genome` tab completion. | 29 July 2015, 12:19:21 UTC |
| e18cb9a | APipe Tester | 29 July 2015, 12:17:30 UTC | Updated class browser cache. | 29 July 2015, 12:17:30 UTC |
| bc87355 | Eddie Belter | 29 July 2015, 01:43:35 UTC | BedTools: use perl built-in version handling | 29 July 2015, 01:43:35 UTC |
| 1632741 | Eddie Belter | 29 July 2015, 01:42:57 UTC | Genotype Concordance: rm default value for bedtools version, add it to doc as recommended | 29 July 2015, 01:42:57 UTC |
| bd0a93b | Eddie Belter | 28 July 2015, 22:15:43 UTC | Merge pull request #889 from ebelter/rm-iferg RM Refs to iferguso and Related Clean Up | 28 July 2015, 22:15:43 UTC |
| 4b357c2 | Eddie Belter | 28 July 2015, 22:13:44 UTC | Merge pull request #890 from ebelter/rm-downstream-model-props Model: rm downstream models property and useless test | 28 July 2015, 22:13:44 UTC |
| 1a33525 | Thomas B. Mooney | 28 July 2015, 21:54:15 UTC | Merge pull request #884 from iferguson90/errorrate Update BamQC to use packaged bam-errorrate | 28 July 2015, 21:54:15 UTC |
| bd099ec | apregier | 28 July 2015, 21:49:11 UTC | Use error_message | 28 July 2015, 21:49:11 UTC |
| f974a2e | apregier | 28 July 2015, 20:21:30 UTC | Use Genome::Sys->open_file_for_reading instead of IO::File | 28 July 2015, 20:21:30 UTC |
| 90aa684 | apregier | 28 July 2015, 20:18:30 UTC | Refactor: access property from class directly | 28 July 2015, 20:18:30 UTC |
| 7430213 | apregier | 28 July 2015, 20:16:49 UTC | Use perl shortcut for chomping an array | 28 July 2015, 20:16:49 UTC |
| 56d6c1f | apregier | 28 July 2015, 20:15:54 UTC | Check whether output filehandle exists | 28 July 2015, 20:15:54 UTC |
| a653e09 | Thomas B. Mooney | 28 July 2015, 17:39:15 UTC | Merge pull request #879 from tmooney/disconnect_dbh_before_long_waiting_things Disconnect Database Handles before potentially long-running actions | 28 July 2015, 17:39:15 UTC |
| c3125a1 | Thomas B. Mooney | 28 July 2015, 14:46:06 UTC | Merge pull request #865 from tmooney/deduplicate_reference_indices Deduplicate Aligner and Annotation Index Classes | 28 July 2015, 14:46:06 UTC |
| 838ccdb | Jason Walker | 28 July 2015, 14:13:13 UTC | Merge pull request #851 from jasonwalker80/library_duplication_rates Library Duplication Rates from Reference Alignment builds | 28 July 2015, 14:13:13 UTC |
| 76043d8 | Thomas Mooney | 28 July 2015, 14:12:54 UTC | Include a newline in printed message. | 28 July 2015, 14:12:54 UTC |
| 940d4cd | Thomas Mooney | 28 July 2015, 14:12:12 UTC | Refer to correct key when getting counts. | 28 July 2015, 14:12:12 UTC |
| a406746 | Thomas Mooney | 28 July 2015, 14:11:53 UTC | Whitespace. | 28 July 2015, 14:11:53 UTC |
| be673d7 | Thomas Mooney | 28 July 2015, 13:17:46 UTC | Only schedule annotation if we have variants to annotate. | 28 July 2015, 13:17:46 UTC |
| 2079ea5 | Eddie Belter | 27 July 2015, 19:40:52 UTC | Model: rm _model_value from Input | 27 July 2015, 19:40:52 UTC |
| ed245d3 | APipe Tester | 27 July 2015, 18:27:24 UTC | updated jenkins submodule to 6a39f4b | 27 July 2015, 19:22:27 UTC |
| 95bdd7c | Eddie Belter | 27 July 2015, 19:11:06 UTC | BedTools: uncapitalize Version in function name | 27 July 2015, 19:11:12 UTC |
| adb61bc | Eddie Belter | 27 July 2015, 19:01:21 UTC | Model: rm downstream models property and test that did not really test anything | 27 July 2015, 19:01:21 UTC |
| 940b82b | Eddie Belter | 27 July 2015, 18:54:59 UTC | Merge pull request #878 from ebelter/model-rm-trigger-downstream-models Model: remove unused _trigger_downstream_builds | 27 July 2015, 18:54:59 UTC |
| 6993458 | Eddie Belter | 27 July 2015, 18:51:07 UTC | AR Bfast: rm iferguso TODO | 27 July 2015, 18:51:07 UTC |
| ca5205b | Eddie Belter | 27 July 2015, 18:50:02 UTC | AR Mosaik: rm iferguso TODOs | 27 July 2015, 18:50:02 UTC |
| 9b3df87 | Eddie Belter | 27 July 2015, 18:49:16 UTC | AR Crossmatch: remove non-matching command that is never run | 27 July 2015, 18:49:16 UTC |
| 0ac0e26 | Eddie Belter | 27 July 2015, 18:47:11 UTC | AR Crossmatch: remove iferguso comments | 27 July 2015, 18:47:11 UTC |
| 2db6279 | Eddie Belter | 27 July 2015, 18:43:42 UTC | AR Crossmatch: remove fastq file check | 27 July 2015, 18:43:42 UTC |
| afbb7f4 | Eddie Belter | 27 July 2015, 18:40:24 UTC | AR Crossmatch: fix indent | 27 July 2015, 18:40:24 UTC |
| 92ee5f8 | Eddie Belter | 27 July 2015, 18:36:54 UTC | AR BLAT: add 1; | 27 July 2015, 18:36:54 UTC |
| 40353bb | Eddie Belter | 27 July 2015, 18:36:00 UTC | AR BLAT: blast2sam.pl is now packaged | 27 July 2015, 18:36:00 UTC |
| 7c41446 | Eddie Belter | 27 July 2015, 18:35:12 UTC | AR BLAT: rm unneeded comments and commented out code | 27 July 2015, 18:35:12 UTC |
| 2b4c96a | Eddie Belter | 27 July 2015, 18:30:55 UTC | RM Iferguso: remove from under allocated email | 27 July 2015, 18:30:55 UTC |
| 513b692 | Avinash Ramu | 27 July 2015, 15:02:51 UTC | Merge pull request #849 from gatoravi/loh_plot_update Remove unwanted points from LOH plot | 27 July 2015, 15:02:51 UTC |
| 3d18bdc | Thomas Mooney | 27 July 2015, 14:21:09 UTC | IDs could be non-numeric these days. | 27 July 2015, 14:21:09 UTC |
| ba5f374 | Thomas B. Mooney | 27 July 2015, 14:19:17 UTC | Merge pull request #877 from tmooney/fix_microarray_dependent_model_check Fix Microarray dependent model check | 27 July 2015, 14:19:17 UTC |
| ac7459a | Thomas Mooney | 27 July 2015, 14:15:18 UTC | Also disconnect before waiting on PTero workflow. | 27 July 2015, 14:15:18 UTC |
| 2b27910 | Thomas B. Mooney | 27 July 2015, 14:11:09 UTC | Merge pull request #885 from tmooney/workflowbuilder_streamgraph_uses_shellcmd Use shellcmd instead of IPC::Run. | 27 July 2015, 14:11:09 UTC |
| 2c006d8 | APipe Tester | 26 July 2015, 18:51:41 UTC | updated ur submodule to b40400c | 26 July 2015, 18:51:41 UTC |
| 6fa7a43 | APipe Tester | 25 July 2015, 12:17:43 UTC | Updated `genome` tab completion. | 25 July 2015, 12:17:43 UTC |
| aa66c27 | APipe Tester | 25 July 2015, 12:15:43 UTC | Updated class browser cache. | 25 July 2015, 12:15:43 UTC |
| c017835 | David Morton | 25 July 2015, 03:58:49 UTC | Merge pull request #888 from davidlmorton/control_flow PTero: Control flow feature | 25 July 2015, 03:58:49 UTC |
| 59250e1 | dmorton | 24 July 2015, 22:12:16 UTC | Update test data for libptero-perl 0.1.7+ The json representation of a workflow changed with respect to how the links section is encoded. | 24 July 2015, 22:12:16 UTC |
| 533cddb | dmorton | 24 July 2015, 22:06:02 UTC | Update how we build PTero workflows for sdk 0.1.7+ libptero-perl 0.1.7 changed the api related to defining links so that more than one data-flow could be defined between a pair of tasks. | 24 July 2015, 22:06:02 UTC |
| f385e25 | dmorton | 24 July 2015, 22:03:22 UTC | Add test that can be run for Genome::Processes This isn't an automated perl-test but it is a Process that you can run manually. It was useful for making sure Genome::Processes can be run with both legacy workflow as well as PTero without testing using a variant-report or something computationally expensive/complex. | 24 July 2015, 22:05:56 UTC |
| d89fe02 | apregier | 08 July 2015, 15:38:13 UTC | Use error messages when assumptions aren't met | 24 July 2015, 18:15:14 UTC |
| 8ac23f8 | apregier | 08 July 2015, 15:37:34 UTC | Only evaluate min_hit requirements with true positives | 24 July 2015, 18:15:14 UTC |
| 068a99b | apregier | 07 July 2015, 19:26:19 UTC | Optionally include true positives in the json output | 24 July 2015, 18:15:13 UTC |
| 04e577a | apregier | 07 July 2015, 19:03:57 UTC | Move into a subtest | 24 July 2015, 18:15:13 UTC |
| 7820105 | apregier | 07 July 2015, 19:02:38 UTC | Allow min_hit_support and true_positive_file to be passed in the config file | 24 July 2015, 18:15:12 UTC |
| 61b887c | apregier | 07 July 2015, 18:57:46 UTC | Optionally output true positives in a file | 24 July 2015, 18:15:11 UTC |
| 8e4ed2d | apregier | 07 July 2015, 18:34:26 UTC | Add an option to require >1 hit in the gold bedpe to count as true positive | 24 July 2015, 18:15:11 UTC |
| 9290125 | apregier | 07 July 2015, 18:33:48 UTC | Fix order of expected and actual results in is_deeply | 24 July 2015, 18:15:10 UTC |
| a21e99d | Eddie Belter | 23 July 2015, 22:54:54 UTC | GM Conordance: add and use available bed tools versions | 23 July 2015, 22:54:54 UTC |
| 76a1223 | Eddie Belter | 23 July 2015, 22:54:10 UTC | Bed Tools: add latest and available versions | 23 July 2015, 22:54:10 UTC |
| 0594bc1 | Eddie Belter | 23 July 2015, 22:51:54 UTC | GM Conordance: add available picard versions | 23 July 2015, 22:51:54 UTC |
| 99ed1cc | Thomas Mooney | 23 July 2015, 21:45:01 UTC | Use shellcmd instead of IPC::Run | 23 July 2015, 21:45:01 UTC |
| 1dcf781 | Eddie Belter | 23 July 2015, 21:38:49 UTC | Genotype Concordance: add use test | 23 July 2015, 21:38:49 UTC |
| fb80c81 | Ian Ferguson | 23 July 2015, 20:12:02 UTC | Update BamQC to use packaged bam-errorrate | 23 July 2015, 20:12:02 UTC |
| 80e97c0 | Eddie Belter | 23 July 2015, 19:48:57 UTC | Merge pull request #875 from ebelter/model-define Model define.t simplification | 23 July 2015, 19:48:57 UTC |
| 9fa15e8 | David Morton | 23 July 2015, 19:36:34 UTC | Merge pull request #883 from davidlmorton/ptero_sdk_1_6_update Update test-data for Ptero sdk version 0.1.6 | 23 July 2015, 19:36:34 UTC |
| ef18dbd | dmorton | 23 July 2015, 19:34:49 UTC | Update test-data for Ptero sdk version 0.1.6 This version introduced the 'dataFlow' syntax to the link definitions. | 23 July 2015, 19:34:49 UTC |
| b94f072 | Thomas Mooney | 23 July 2015, 13:42:40 UTC | Disconnect dbh before launching readcounts workflow. | 23 July 2015, 13:42:40 UTC |
| 77a3c5e | Thomas Mooney | 22 July 2015, 21:32:52 UTC | Dump flagstat data if it doesn't match. | 22 July 2015, 21:32:52 UTC |
| 2c81ebe | Thomas Mooney | 22 July 2015, 21:00:39 UTC | Disconnect DBH before submitting workflow. This won't return until it's done. | 22 July 2015, 21:00:39 UTC |
| 7576d58 | Thomas Mooney | 22 July 2015, 21:00:06 UTC | Disconnect from DB before locking. We might be waiting hours or days... | 22 July 2015, 21:00:06 UTC |
| 6cf073a | Thomas B. Mooney | 22 July 2015, 20:07:13 UTC | Merge pull request #874 from tmooney/send_to_pap_wf_errors_are_errors Use error_message for SendToPap's Workflow Errors | 22 July 2015, 20:07:13 UTC |
| 26913ed | Eddie Belter | 22 July 2015, 19:15:36 UTC | Build: rm _trigger_downstream_builds call | 22 July 2015, 19:15:36 UTC |
| 98b4c76 | Thomas Mooney | 22 July 2015, 15:32:57 UTC | Model IDs aren't numeric. | 22 July 2015, 15:32:57 UTC |
| 2352e7a | Thomas Mooney | 22 July 2015, 15:32:38 UTC | Fix precedence in dependent model logic. | 22 July 2015, 15:32:38 UTC |
| d6c983f | Eddie Belter | 21 July 2015, 22:45:20 UTC | Model: remove unused _trigger_downstream_builds | 21 July 2015, 22:45:20 UTC |
| f317fec | Eddie Belter | 21 July 2015, 22:42:42 UTC | Model Define: use sub tests | 21 July 2015, 22:42:42 UTC |
| 8103702 | Eddie Belter | 21 July 2015, 22:37:26 UTC | Model Define: simplify accessor tests | 21 July 2015, 22:37:26 UTC |
| 5a887a0 | Eddie Belter | 21 July 2015, 22:24:28 UTC | Model Define: rm skipped tests | 21 July 2015, 22:24:28 UTC |
| 1675d1c | Eddie Belter | 21 July 2015, 22:06:23 UTC | Model Define: rm unsed variables | 21 July 2015, 22:07:06 UTC |
| e662f08 | Eddie Belter | 21 July 2015, 22:03:52 UTC | Model Define: merge tests | 21 July 2015, 22:03:52 UTC |
| 7456189 | Eddie Belter | 21 July 2015, 22:03:47 UTC | Model Define: merge tests | 21 July 2015, 22:03:47 UTC |
| 12db73e | Eddie Belter | 21 July 2015, 21:54:52 UTC | Model Define: test processing profile directly | 21 July 2015, 21:54:52 UTC |
| 0d21a8a | Eddie Belter | 21 July 2015, 21:52:03 UTC | Model Define: use define class instead of deriving it | 21 July 2015, 21:52:03 UTC |
| ecb246a | Eddie Belter | 21 July 2015, 21:49:38 UTC | Model Define: use test factory for reseq | 21 July 2015, 21:49:38 UTC |
| bf0b04b | Eddie Belter | 21 July 2015, 21:42:36 UTC | Model Define: no more convergence models | 21 July 2015, 21:42:36 UTC |
| de6cb80 | Eddie Belter | 21 July 2015, 21:41:57 UTC | Model Define: pass model group objects | 21 July 2015, 21:41:57 UTC |
| 28e8555 | Eddie Belter | 21 July 2015, 21:36:18 UTC | Model Define: rm unneeded test creating model w/ diff refseq | 21 July 2015, 21:37:10 UTC |
| 190d76e | Eddie Belter | 21 July 2015, 21:33:12 UTC | Model Define: rm test_model_from_params and call successful_create_model directly | 21 July 2015, 21:33:21 UTC |
