| 955abe3 | Ben Oberkfell | 24 June 2013, 21:16:40 UTC | Allocations cannot be archived if they are less than 1GB. Don't try to sweep up allocations smaller than that. | 24 June 2013, 22:10:54 UTC |
| b44138e | APipe Tester | 24 June 2013, 21:45:17 UTC | Updated `gmt` tab completion. | 24 June 2013, 21:45:48 UTC |
| beeacdd | APipe Tester | 24 June 2013, 21:43:56 UTC | Updated `genome` tab completion. | 24 June 2013, 21:45:48 UTC |
| dbd93ac | APipe Tester | 24 June 2013, 21:41:49 UTC | Updated class browser cache. | 24 June 2013, 21:45:48 UTC |
| b6fb6ab | Mark Burnett | 24 June 2013, 21:37:16 UTC | fix typo in debug message | 24 June 2013, 21:37:16 UTC |
| 436ba90 | Travis Abbott | 24 June 2013, 21:25:43 UTC | add breakdancer 1.4.1 | 24 June 2013, 21:25:43 UTC |
| 39f767b | Nathan Nutter | 24 June 2013, 16:19:04 UTC | add initial apipe-test-reference-alignment-lane-qc and sort | 24 June 2013, 16:19:21 UTC |
| d15eaf3 | APipe Tester | 24 June 2013, 15:54:00 UTC | Updated `gmt` tab completion. | 24 June 2013, 15:54:00 UTC |
| ecb969b | APipe Tester | 24 June 2013, 15:53:06 UTC | Updated `genome` tab completion. | 24 June 2013, 15:53:06 UTC |
| 33a9b50 | APipe Tester | 24 June 2013, 15:51:26 UTC | Updated class browser cache. | 24 June 2013, 15:51:26 UTC |
| 3a92d3e | APipe Tester | 24 June 2013, 15:33:30 UTC | updated ur submodule to a585e50 | 24 June 2013, 15:33:30 UTC |
| 4746ab6 | Scott Smith | 24 June 2013, 15:28:37 UTC | Cleanup Genome::Model::Build API. | 24 June 2013, 15:28:37 UTC |
| a805a72 | APipe Tester | 24 June 2013, 09:52:55 UTC | updated ur submodule to 0ecac19 | 24 June 2013, 09:52:55 UTC |
| 777197f | Nathan Nutter | 23 June 2013, 21:23:44 UTC | hotfix lane QC models not being startable | 23 June 2013, 21:23:44 UTC |
| 8c80e37 | Nathan Nutter | 21 June 2013, 23:37:10 UTC | use compare_ok to get free diff | 21 June 2013, 23:37:35 UTC |
| 86656f6 | Nathan Nutter | 21 June 2013, 22:25:16 UTC | use compare_ok to get free diff | 21 June 2013, 23:37:35 UTC |
| a301a76 | Nathan Nutter | 21 June 2013, 22:24:31 UTC | regenerate expected output due to change in Command | 21 June 2013, 23:37:34 UTC |
| 1520e8d | Nathan Nutter | 21 June 2013, 20:18:11 UTC | $ENV changes should probably always be localized | 21 June 2013, 23:37:34 UTC |
| 470d437 | Nathan Nutter | 21 June 2013, 20:17:26 UTC | use local instead of setting and unsetting | 21 June 2013, 23:37:33 UTC |
| 6aa9a2e | Nathan Nutter | 21 June 2013, 20:13:53 UTC | enable more logging for builds | 21 June 2013, 23:37:33 UTC |
| f5e969f | Adam Coffman | 21 June 2013, 20:55:50 UTC | t pushMerge branch 'master' of ssh://git/srv/git/genome | 21 June 2013, 20:55:50 UTC |
| 3c483af | Adam Coffman | 21 June 2013, 20:53:35 UTC | Make it so that AQID will not unintentionally process instrument data it shouldnt | 21 June 2013, 20:53:35 UTC |
| 94b9531 | APipe Tester | 21 June 2013, 20:15:43 UTC | updated ur submodule to 813d1e5 | 21 June 2013, 20:15:43 UTC |
| 52d3f92 | APipe Tester | 21 June 2013, 15:56:49 UTC | Updated `gmt` tab completion. | 21 June 2013, 15:56:49 UTC |
| 31c7906 | APipe Tester | 21 June 2013, 15:55:45 UTC | Updated `genome` tab completion. | 21 June 2013, 15:55:45 UTC |
| e45eb31 | APipe Tester | 21 June 2013, 15:52:15 UTC | Updated class browser cache. | 21 June 2013, 15:52:15 UTC |
| 5ca67bf | Chris Miller | 21 June 2013, 15:38:01 UTC | bugfix | 21 June 2013, 15:38:39 UTC |
| 371a4b7 | Chris Miller | 21 June 2013, 15:37:55 UTC | rfile dumping option and bugfix | 21 June 2013, 15:38:37 UTC |
| 034cb23 | Nathan Nutter | 21 June 2013, 14:34:20 UTC | bytes not bits | 21 June 2013, 14:34:35 UTC |
| c706e81 | APipe Tester | 20 June 2013, 22:23:32 UTC | Updated `genome` tab completion. | 20 June 2013, 22:23:32 UTC |
| 365e5f2 | APipe Tester | 20 June 2013, 22:21:24 UTC | Updated class browser cache. | 20 June 2013, 22:21:24 UTC |
| c0ac098 | Ben Oberkfell | 20 June 2013, 21:56:06 UTC | add command to archive expired allocations | 20 June 2013, 21:58:20 UTC |
| 7bf7f2c | Ben Oberkfell | 20 June 2013, 21:54:45 UTC | add archive_after_time to allowable create params | 20 June 2013, 21:58:20 UTC |
| f722b37 | APipe Tester | 20 June 2013, 19:34:41 UTC | Updated `genome` tab completion. | 20 June 2013, 19:34:41 UTC |
| b4bd36e | APipe Tester | 20 June 2013, 19:32:27 UTC | Updated class browser cache. | 20 June 2013, 19:32:27 UTC |
| c594775 | Eddie Belter | 20 June 2013, 19:21:51 UTC | Sample Import Manager: use test data dir | 20 June 2013, 19:21:51 UTC |
| 861b73a | Eddie Belter | 20 June 2013, 18:50:57 UTC | Sample Import Manager: update doc | 20 June 2013, 18:51:52 UTC |
| 9d1c269 | Eddie Belter | 20 June 2013, 18:25:36 UTC | Sample Import Manager: actually launch inst data command | 20 June 2013, 18:51:52 UTC |
| 1915557 | Eddie Belter | 20 June 2013, 18:19:31 UTC | Sample Import Manager: launch inst data import command method; do not set inst data import cmd on sample; | 20 June 2013, 18:51:51 UTC |
| ad8614f | Eddie Belter | 20 June 2013, 17:16:45 UTC | Sample Import Manager: get imst data import command working | 20 June 2013, 18:51:51 UTC |
| 93b2ac5 | Eddie Belter | 03 June 2013, 21:55:08 UTC | Sample Manager: rename status-onyl to make-progress; add test for this | 20 June 2013, 18:51:50 UTC |
| 8261950 | Eddie Belter | 03 June 2013, 21:46:07 UTC | Sample Manager: move create sample/model to make progress method | 20 June 2013, 18:51:50 UTC |
| 55c2a2e | Eddie Belter | 03 June 2013, 21:33:47 UTC | Sample Manager: move resolve inst data import cmd to __errors__ | 20 June 2013, 18:51:49 UTC |
| 428bc15 | Eddie Belter | 03 June 2013, 21:20:27 UTC | Sample Manager: move resolve model params into __errors__ | 20 June 2013, 18:51:49 UTC |
| 976a6f3 | Eddie Belter | 29 May 2013, 17:58:05 UTC | Sample Manager: get inst data archive path or bam path; run import cmd or build as necessary | 20 June 2013, 18:51:49 UTC |
| 1e3e01c | Eddie Belter | 28 May 2013, 18:29:34 UTC | Sample Manager: can specify inst data attrs in samples.csv | 20 June 2013, 18:51:48 UTC |
| abb662d | Eddie Belter | 28 May 2013, 16:36:49 UTC | Sample Manager: rename original_data_path to source_files; create import command | 20 June 2013, 18:51:48 UTC |
| 386ab39 | Eddie Belter | 24 May 2013, 20:52:57 UTC | Sample Manager: ensure auto_ stuff is off for model; join original_data_path with commas when getting inst data | 20 June 2013, 18:51:47 UTC |
| 6f5744e | Eddie Belter | 24 May 2013, 20:39:19 UTC | Sample Import: add WHIM to config | 20 June 2013, 18:51:47 UTC |
| 3c7597a | Eddie Belter | 24 May 2013, 20:38:56 UTC | Sample Manager: complete loading samples and models; add status-only property | 20 June 2013, 18:51:46 UTC |
| 913298b | Eddie Belter | 23 May 2013, 21:33:44 UTC | Sample Manager: rm functions property | 20 June 2013, 18:51:46 UTC |
| c430853 | Eddie Belter | 23 May 2013, 21:32:42 UTC | Sample Manager: update test to pass | 20 June 2013, 18:51:45 UTC |
| 7664c03 | Eddie Belter | 23 May 2013, 21:27:13 UTC | Sample Manager: set inst data and bam path on samples hash | 20 June 2013, 18:51:45 UTC |
| db0db5c | Eddie Belter | 23 May 2013, 21:20:49 UTC | Sample Manager: get or create model when loading samples | 20 June 2013, 18:51:45 UTC |
| f221ceb | Eddie Belter | 23 May 2013, 21:14:31 UTC | Sample Manager: get or create genome sample when loading samples | 20 June 2013, 18:51:44 UTC |
| dc9f4db | Eddie Belter | 23 May 2013, 20:34:33 UTC | Sample Manager: get objects for model params | 20 June 2013, 18:51:44 UTC |
| c639ac6 | Eddie Belter | 23 May 2013, 20:15:32 UTC | Sample Manager: collect params to create model | 20 June 2013, 18:51:43 UTC |
| 87766c4 | Eddie Belter | 23 May 2013, 20:08:14 UTC | Sample Manager: start editing create_models | 20 June 2013, 18:51:43 UTC |
| 6df39b2 | Eddie Belter | 23 May 2013, 19:24:58 UTC | Sample Manager: complete sample creation | 20 June 2013, 18:51:42 UTC |
| cada138 | Eddie Belter | 23 May 2013, 19:10:52 UTC | Sample Manager: update sample create | 20 June 2013, 18:51:42 UTC |
| 8dd5144 | Eddie Belter | 22 May 2013, 18:46:39 UTC | Sample Import: set importer_property_names to empty aryref | 20 June 2013, 18:51:42 UTC |
| 84bf8cb | Eddie Belter | 22 May 2013, 18:45:53 UTC | Sample Manager: rm bak file | 20 June 2013, 18:51:41 UTC |
| 4f139ee | Eddie Belter | 20 May 2013, 20:59:46 UTC | Sample Import: add methods to get importer class adn properties for namespace | 20 June 2013, 18:51:41 UTC |
| 695081e | Eddie Belter | 20 May 2013, 19:29:53 UTC | Sample Manager: load sample csv file before execute | 20 June 2013, 18:51:40 UTC |
| 2f5da7b | Eddie Belter | 20 May 2013, 19:19:06 UTC | Sample Manager: load config before execute; add namespace and importer class name properties | 20 June 2013, 18:51:40 UTC |
| 7065f05 | Eddie Belter | 20 May 2013, 18:56:29 UTC | Sample Import: add getting namespace for nomenclature | 20 June 2013, 18:51:39 UTC |
| 6a74b6c | Eddie Belter | 20 May 2013, 18:41:44 UTC | Sample Manager: add namespace to test | 20 June 2013, 18:51:39 UTC |
| 1819a25 | Eddie Belter | 20 May 2013, 16:44:19 UTC | Sample Import: store import config and property names to be used by the sample import manager | 20 June 2013, 18:51:38 UTC |
| 9427cd7 | Eddie Belter | 16 May 2013, 21:10:05 UTC | Sample Manager: add tests for config file and sample csv existing | 20 June 2013, 18:51:38 UTC |
| 12c9323 | Eddie Belter | 16 May 2013, 21:06:17 UTC | Sample Manager: samples are a property that is a hash | 20 June 2013, 18:51:37 UTC |
| e41b812 | Eddie Belter | 16 May 2013, 20:29:45 UTC | Sample Manager: config file is YAML, is loaded inn _errors__ and has model and job config | 20 June 2013, 18:51:37 UTC |
| 1247b70 | Eddie Belter | 02 May 2013, 20:36:08 UTC | Sample Import Manager: require original data path in samples csv | 20 June 2013, 18:51:37 UTC |
| 19519c9 | Eddie Belter | 02 May 2013, 20:31:02 UTC | Sample Import Manager: add inst data and model getting for load samples | 20 June 2013, 18:51:36 UTC |
| 77c4a87 | Eddie Belter | 02 May 2013, 19:44:33 UTC | Sample Import Manager: update get/set sample status method | 20 June 2013, 18:51:36 UTC |
| 4d8b5c8 | Eddie Belter | 02 May 2013, 19:19:56 UTC | Sample Import Manager: move job status into separate method | 20 June 2013, 18:51:35 UTC |
| ae2f1e7 | Eddie Belter | 01 May 2013, 20:48:51 UTC | Sample Import Manager: _load_samples works | 20 June 2013, 18:51:35 UTC |
| e6eabf6 | Eddie Belter | 01 May 2013, 20:19:32 UTC | Sample Import Manager: update sample data structure when loading from csv | 20 June 2013, 18:51:34 UTC |
| fb400b8 | Eddie Belter | 01 May 2013, 20:00:15 UTC | Sample Import Manager: add load from sample csv | 20 June 2013, 18:51:34 UTC |
| 7b715e2 | Eddie Belter | 01 May 2013, 19:26:16 UTC | Sample Import Manager: initial commit | 20 June 2013, 18:51:33 UTC |
| b5bc0bc | APipe Tester | 20 June 2013, 18:37:58 UTC | Updated `gmt` tab completion. | 20 June 2013, 18:37:58 UTC |
| 5d5b89c | APipe Tester | 20 June 2013, 18:36:40 UTC | Updated `genome` tab completion. | 20 June 2013, 18:36:40 UTC |
| d56018c | APipe Tester | 20 June 2013, 18:33:03 UTC | Updated class browser cache. | 20 June 2013, 18:33:03 UTC |
| d998415 | Thomas Mooney | 20 June 2013, 18:06:46 UTC | Make reference-transcripts non-optional. The params to `gmt annotate transcript-variants` get mangled otherwise. | 20 June 2013, 18:14:10 UTC |
| cccc34a | Nathan Nutter | 20 June 2013, 14:54:35 UTC | Merge branch 'anti-spam' CHANGELOG: In an attempt to reduce the amount of information that gets spammed to the screen when you start a reference alignment model we have suppressed many messages that really only need to be displayed for debugging purposes. Next time you start a reference alignment model you may feel like something is wrong because you are used to those messages but we hope that this will provide a better experience. | 20 June 2013, 18:04:37 UTC |
| 871810c | Nathan Nutter | 19 June 2013, 21:07:50 UTC | make reference_coverage semi-required reference_coverage is only required if there are reference_coverage_objects, e.g. a region_of_interest_set_name. | 20 June 2013, 17:51:34 UTC |
| b427546 | Nathan Nutter | 19 June 2013, 19:25:48 UTC | change some status_message to debug_message These can be changed back if needed. We still don't have an easy way to show debug messages (or to log them). These messages were switched due to TCGA reference alignment builds spitting out hundreds of lines of messages. | 20 June 2013, 17:51:33 UTC |
| 8f80498 | APipe Tester | 20 June 2013, 17:31:05 UTC | updated ur submodule to 66f7fc1 | 20 June 2013, 17:31:05 UTC |
| 2146354 | Ian Ferguson | 20 June 2013, 16:25:33 UTC | Increase bwamem tmp space lsf resource request | 20 June 2013, 16:25:33 UTC |
| dc0e8e3 | Scott Smith | 19 June 2013, 22:27:11 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 19 June 2013, 22:27:11 UTC |
| 71441bb | Scott Smith | 19 June 2013, 22:25:21 UTC | Updated Strelka to work with v1.0.7. Strelka.t now also tests 1.0.7, and uses the correct data dir. Previous tests were using "DetectVariants-" instead of "DetectVariants2-" as the test directory. | 19 June 2013, 22:25:21 UTC |
| c05428a | Ian Ferguson | 19 June 2013, 22:14:53 UTC | Approve indel diffs in somatic-validation test | 19 June 2013, 22:15:10 UTC |
| 24deccd | Ian Ferguson | 19 June 2013, 22:14:02 UTC | Approve indel diffs in somatic-variation-short test | 19 June 2013, 22:15:08 UTC |
| 33e43c8 | Mark Burnett | 19 June 2013, 21:25:06 UTC | bugfix: M:SVar:C:Anno&UpVars -> used uninitialized variable | 19 June 2013, 21:27:57 UTC |
| 8e55b9e | Adam Coffman | 19 June 2013, 21:24:34 UTC | whitespace fix | 19 June 2013, 21:24:34 UTC |
| 3ee9fc9 | Adam Coffman | 19 June 2013, 21:18:22 UTC | loading an object shouldnt update its timestamp | 19 June 2013, 21:18:22 UTC |
| 34c86b5 | Ian Ferguson | 19 June 2013, 20:28:15 UTC | Approve indel diffs in reference-alignment test | 19 June 2013, 20:28:24 UTC |
| cfd72b7 | Todd Hepler | 19 June 2013, 20:05:39 UTC | try to download faster | 19 June 2013, 20:05:39 UTC |
| 6a7a668 | Todd Hepler | 19 June 2013, 19:48:35 UTC | preparing for GeneTorrent version 3.8.3 | 19 June 2013, 19:48:51 UTC |
| 7249884 | apregier | 19 June 2013, 19:45:30 UTC | Do not request builds for tcga-bam imports | 19 June 2013, 19:45:48 UTC |
| 4faa45e | APipe Tester | 19 June 2013, 19:43:22 UTC | updated ur submodule to 1060c84 | 19 June 2013, 19:43:22 UTC |
