d8b039e | Dave Larson | 03 December 2014, 16:42:50 UTC | Merge pull request #256 from ernfrid/handle_no_repeats Handle no repeats found in EGAP. | 03 December 2014, 16:42:50 UTC |
b9a46af | Dave Larson | 03 December 2014, 16:40:01 UTC | remove comment litter | 03 December 2014, 16:40:01 UTC |
27079a3 | Dave Larson | 03 December 2014, 16:31:29 UTC | minor refactor of handling of no-repetitive sequences detected to give better log file output | 03 December 2014, 16:31:29 UTC |
a61b0cb | Thomas B. Mooney | 03 December 2014, 16:19:26 UTC | Merge pull request #253 from tmooney/better_subjectmapping_errors Really die if we don't find a subject. | 03 December 2014, 16:19:26 UTC |
4b1a7fc | APipe Tester | 03 December 2014, 15:48:08 UTC | Merge pull request #246 from jasonwalker80/picard_revert_sam_updates | 03 December 2014, 15:48:08 UTC |
c4463fe | APipe Tester | 03 December 2014, 15:42:48 UTC | Merge pull request #210 from jasonwalker80/rna_ercc_qc | 03 December 2014, 15:42:48 UTC |
7a37b4b | APipe Tester | 03 December 2014, 13:15:37 UTC | Updated `genome` tab completion. | 03 December 2014, 13:15:37 UTC |
47192e7 | APipe Tester | 03 December 2014, 13:14:02 UTC | Updated class browser cache. | 03 December 2014, 13:14:02 UTC |
8615562 | Dave Larson | 02 December 2014, 21:48:45 UTC | test handling no repeats by copying the input fasta | 02 December 2014, 21:48:45 UTC |
c32fe7e | Thomas Mooney | 02 December 2014, 16:17:01 UTC | Really die if we don't find a subject. | 02 December 2014, 16:17:01 UTC |
d942c18 | Thomas B. Mooney | 02 December 2014, 15:40:47 UTC | Merge pull request #252 from tmooney/dont_inherit_mc16s_commands Fix MC16s copy-files inheritance | 02 December 2014, 15:40:47 UTC |
82ca05b | APipe Tester | 02 December 2014, 13:16:16 UTC | Updated `genome` tab completion. | 02 December 2014, 13:16:16 UTC |
c4b0f8f | Thomas Mooney | 01 December 2014, 20:36:01 UTC | Pull down base options since only one command inherits. | 01 December 2014, 20:57:12 UTC |
40043e2 | Thomas Mooney | 01 December 2014, 20:31:44 UTC | Split out base class features from Tree command. | 01 December 2014, 20:57:12 UTC |
f377264 | David Morton | 01 December 2014, 19:12:34 UTC | Merge pull request #245 from davidlmorton/translated_plans Translated plans | 01 December 2014, 19:12:34 UTC |
a0b44a4 | Jason Walker | 01 December 2014, 18:12:09 UTC | Added back a few more is_optional values for default attributes. | 01 December 2014, 18:12:09 UTC |
76ffb5f | Jason Walker | 01 December 2014, 18:04:51 UTC | A couple class definition changes and an update to the sanitize picard version comparison to include v1.108 | 01 December 2014, 18:04:51 UTC |
c4e321b | Malachi Griffith | 01 December 2014, 17:19:39 UTC | Merge pull request #249 from malachig/master clinseq: add additional filtering options to snv-indel-report and related clean up | 01 December 2014, 17:19:39 UTC |
ea2cb07 | apregier | 01 December 2014, 14:54:04 UTC | Merge pull request #242 from apregier/labeled_result_users Labeled result users | 01 December 2014, 14:54:04 UTC |
7c6f362 | Malachi Griffith | 26 November 2014, 23:48:05 UTC | clin-seq: bless new build of clinseq-test-wer to take into account updates to snv-indel-report filtering | 26 November 2014, 23:48:05 UTC |
f413771 | Malachi Griffith | 26 November 2014, 22:53:55 UTC | clin-seq: update test results for snv-indel-report test | 26 November 2014, 22:53:55 UTC |
c0d6bd7 | Malachi Griffith | 26 November 2014, 22:27:35 UTC | clinseq: add optional variant caller count filters to snv-indel-report | 26 November 2014, 22:27:35 UTC |
c175544 | Malachi Griffith | 26 November 2014, 21:37:25 UTC | clin-seq: added min variant read count filter parameter to snv-indel-report | 26 November 2014, 21:37:25 UTC |
b02c8e1 | APipe Tester | 26 November 2014, 21:27:48 UTC | updated jenkins submodule to b914bc4 | 26 November 2014, 21:27:48 UTC |
11708e0 | APipe Tester | 26 November 2014, 21:27:25 UTC | updated ur submodule to 595556a | 26 November 2014, 21:27:25 UTC |
293ee8d | Nathaniel Nutter | 26 November 2014, 21:19:48 UTC | Merge pull request #248 from nnutter/running_testsuites remove use of running_testsuites | 26 November 2014, 21:19:48 UTC |
25341a6 | Malachi Griffith | 26 November 2014, 21:18:50 UTC | clin-seq: improve subject legends file for snv-indel-report and remove redundant code in get_ref_align_builds | 26 November 2014, 21:18:50 UTC |
42ab23d | Dave Larson | 26 November 2014, 20:15:04 UTC | Merge pull request #247 from ernfrid/up_verbosity up the verbosity level for Fgenesh. This will at least give us the comma... | 26 November 2014, 20:15:04 UTC |
05517cc | Malachi Griffith | 26 November 2014, 19:59:49 UTC | clin-seq: make check for sample common name case insensitive | 26 November 2014, 19:59:49 UTC |
30ca5f2 | Nathaniel Nutter | 26 November 2014, 19:57:48 UTC | remove use of running_testsuites These tests were unnecessarily using running_testsuites and the volume running_testsuites points to was recently shrunk down to it's current usage so ClinicalData-db.t could no longer write there. | 26 November 2014, 19:57:48 UTC |
1d82974 | Eddie Belter | 26 November 2014, 19:50:58 UTC | Merge pull request #243 from ebelter/rdp-training-set RDP | 26 November 2014, 19:50:58 UTC |
965bd91 | Jason Walker | 26 November 2014, 19:39:35 UTC | Remove is_optional when default_value is defined. | 26 November 2014, 19:39:35 UTC |
2b0a555 | David Morton | 26 November 2014, 19:24:52 UTC | Merge pull request #241 from davidlmorton/unique_results Add unique_results method | 26 November 2014, 19:24:52 UTC |
90069ca | Jason Walker | 26 November 2014, 18:42:40 UTC | Add correct version parsing. | 26 November 2014, 18:42:40 UTC |
250571d | Jason Walker | 26 November 2014, 17:26:05 UTC | Remove R library dependency on optparse. | 26 November 2014, 17:26:05 UTC |
8a1f30f | Jason Walker | 26 November 2014, 17:08:52 UTC | Add version check for sanitize option. | 26 November 2014, 17:08:52 UTC |
4c8e5fc | Jason Walker | 26 November 2014, 15:45:57 UTC | Fixes to compilation issues. Consistant use of hash_ref instead of dereferencing. Add test case. | 26 November 2014, 15:45:57 UTC |
0af295a | Dave Larson | 26 November 2014, 15:29:52 UTC | up the verbosity level for Fgenesh. This will at least give us the command line in the log file when it fails. | 26 November 2014, 15:29:52 UTC |
f79eb62 | Jason Walker | 26 November 2014, 14:19:32 UTC | Add new params to sanitize BAM file available since Picard 1.108 | 26 November 2014, 14:19:32 UTC |
60af6c5 | dmorton | 26 November 2014, 03:43:40 UTC | Stop passing around provider_json Since we can now just translate the plan and pass around the translated plan, there is no need to pass around the translations as well. | 26 November 2014, 04:43:32 UTC |
41de84a | dmorton | 26 November 2014, 03:36:17 UTC | Move expected.xml files from allocation to repo This will make it less annoying to alter anything that affects the workflow xml that is generated. | 26 November 2014, 04:43:31 UTC |
31df90a | dmorton | 26 November 2014, 02:48:40 UTC | Add requires_annotations to test classes | 26 November 2014, 04:43:31 UTC |
2522b67 | dmorton | 26 November 2014, 02:42:43 UTC | Ensure plans don't get translated more than once. This also makes it clear, if you write out a plan, whether it has been translated or not. | 26 November 2014, 04:43:31 UTC |
811a2f4 | dmorton | 26 November 2014, 02:33:28 UTC | Translate plans instead of objects This has (at least) two benefits: 1) it paves the way to get rid of the provider as a dag input. 2) since we were creating and object, and then translating its params, there was no way to determine the hash of translated params for SoftwareResult subclasses (or anything that does work in create generally). Since we plan to make Reporters into SoftwareResults, this is a big deal. | 26 November 2014, 04:43:30 UTC |
0e3537b | dmorton | 26 November 2014, 02:27:09 UTC | Don't create temporary object for validation | 26 November 2014, 02:27:57 UTC |
6047ab8 | dmorton | 25 November 2014, 18:44:19 UTC | Allow plans to validate providers without objects | 25 November 2014, 18:44:19 UTC |
55ade62 | APipe Tester | 25 November 2014, 13:22:29 UTC | Updated `gmt` tab completion. | 25 November 2014, 13:22:29 UTC |
7827034 | APipe Tester | 25 November 2014, 13:20:52 UTC | Updated `genome` tab completion. | 25 November 2014, 13:20:52 UTC |
b71ebb3 | Eddie Belter | 25 November 2014, 00:34:19 UTC | RDP: allow cli to take training set name or path; rdp versions require an instantiated training set | 25 November 2014, 00:34:19 UTC |
e54b4fa | David Morton | 24 November 2014, 22:06:20 UTC | Merge pull request #240 from davidlmorton/wb_constants Add ability to declare constants to WorkflowBuilder Operations | 24 November 2014, 22:06:20 UTC |
d7de896 | apregier | 24 November 2014, 18:01:35 UTC | DelegateResult accepts a user label | 24 November 2014, 18:13:46 UTC |
ceac1b4 | apregier | 24 November 2014, 17:50:10 UTC | Pass in actual software result rather than using global variable | 24 November 2014, 17:50:10 UTC |
2f044a6 | dmorton | 24 November 2014, 17:18:28 UTC | Add unique_results method This is useful for when there are more than one SoftwareResult::User relationships between the process and the results. | 24 November 2014, 17:18:28 UTC |
a1df181 | Feiyu Du | 24 November 2014, 16:34:01 UTC | Merge pull request #239 from dufeiyu/extract_rg_bam Modify Genome::Model::Tools::Sam::ExtractReadGroup | 24 November 2014, 16:34:01 UTC |
09e33b8 | dmorton | 24 November 2014, 01:26:35 UTC | Automatically add constant_values to execute They can be overridden since @_ comes after them in %inputs. | 24 November 2014, 01:26:35 UTC |
ee8a5c4 | APipe Tester | 23 November 2014, 13:21:50 UTC | Updated `gmt` tab completion. | 23 November 2014, 13:21:50 UTC |
45d56b4 | APipe Tester | 23 November 2014, 13:20:22 UTC | Updated `genome` tab completion. | 23 November 2014, 13:20:22 UTC |
61fcc55 | APipe Tester | 23 November 2014, 13:17:02 UTC | Updated class browser cache. | 23 November 2014, 13:17:02 UTC |
d8ef5df | dmorton | 23 November 2014, 05:20:54 UTC | Add ability to declare constants on Operations Constants cannot be the target of additional links, they automatically connect to the 'input connector'. Constants propagate when the operation is added to a dag via 'add_operation'. | 23 November 2014, 05:31:19 UTC |
71afc0d | dmorton | 22 November 2014, 20:48:58 UTC | Replace is_many with ARRAY type properties 1) performance gain (minor) 2) because we want to add some functionality to add_operation. | 22 November 2014, 20:48:58 UTC |
193affb | Thomas B. Mooney | 22 November 2014, 18:59:59 UTC | Merge pull request #231 from tmooney/copy_profile_status Copy status when copying the profile items. | 22 November 2014, 18:59:59 UTC |
e3c14f3 | Thomas B. Mooney | 22 November 2014, 18:59:42 UTC | Merge pull request #228 from tmooney/deduplicate_gcbase Switch over remaining uses of Genome::Command::Base to Command::V2. CHANGELOG: The GENOME_NO_REQUIRE_USER_VERIFY environment variable no longer has any effect and will be removed in a future snapshot. Control of prompting is consolidated into the existing UR_NO_REQUIRE_USER_VERIFY variable. The UR version of the variable should be used in all cases where the GENOME version was previously. | 22 November 2014, 18:59:42 UTC |
cda7fb3 | APipe Tester | 22 November 2014, 13:21:31 UTC | Updated `gmt` tab completion. | 22 November 2014, 13:21:31 UTC |
39da66b | APipe Tester | 22 November 2014, 13:20:08 UTC | Updated `genome` tab completion. | 22 November 2014, 13:20:08 UTC |
76ac4df | APipe Tester | 22 November 2014, 13:17:06 UTC | Updated class browser cache. | 22 November 2014, 13:17:06 UTC |
11aa168 | jhundal | 21 November 2014, 19:31:41 UTC | Merge pull request #215 from jhundal/master Epitope Prediction : New Module Added | 21 November 2014, 19:31:41 UTC |
592d064 | jhundal | 21 November 2014, 19:00:29 UTC | Merge pull request #1 from nnutter/epitope use SeparatedValueReader and SeparatedValueWriter | 21 November 2014, 19:00:29 UTC |
bd05780 | Nathaniel Nutter | 21 November 2014, 18:03:54 UTC | brackets aren't necessary for single inheritance | 21 November 2014, 18:07:24 UTC |
28e9b68 | Nathaniel Nutter | 21 November 2014, 18:03:03 UTC | whitespace | 21 November 2014, 18:05:04 UTC |
2e1de32 | Nathaniel Nutter | 21 November 2014, 18:02:02 UTC | specifically import basename | 21 November 2014, 18:02:02 UTC |
db37004 | Nathaniel Nutter | 21 November 2014, 18:01:14 UTC | whitespace | 21 November 2014, 18:01:14 UTC |
00d3496 | Feiyu Du | 21 November 2014, 17:54:14 UTC | remove unnecessary variable | 21 November 2014, 17:54:14 UTC |
144d757 | Nathaniel Nutter | 21 November 2014, 17:53:36 UTC | whitespace | 21 November 2014, 17:53:36 UTC |
77d793b | Nathaniel Nutter | 21 November 2014, 17:51:52 UTC | refactor to remove duplicate assignments | 21 November 2014, 17:51:52 UTC |
aa864d5 | Nathaniel Nutter | 21 November 2014, 17:50:42 UTC | refactor to remove duplicated code | 21 November 2014, 17:50:42 UTC |
42ae472 | Nathaniel Nutter | 21 November 2014, 17:49:26 UTC | remove double negative | 21 November 2014, 17:49:26 UTC |
926f43f | Feiyu Du | 21 November 2014, 17:42:11 UTC | change the naming of temp bam file | 21 November 2014, 17:42:11 UTC |
bf581fb | apregier | 21 November 2014, 17:32:37 UTC | Merge pull request #234 from apregier/update-docm-in-vr Use updated docm vcfs in variant reporting | 21 November 2014, 17:32:37 UTC |
40c7c81 | Eddie Belter | 21 November 2014, 17:29:18 UTC | Merge pull request #227 from ebelter/cg-hub Cg Hub | 21 November 2014, 17:29:18 UTC |
9e876e1 | Feiyu Du | 21 November 2014, 17:06:58 UTC | add unit test | 21 November 2014, 17:06:58 UTC |
37ff4f3 | Adam Coffman | 21 November 2014, 15:37:01 UTC | Merge pull request #232 from acoffman/add_default_starting_status_for_config_items Add default starting status for config items | 21 November 2014, 15:37:01 UTC |
ee88209 | APipe Tester | 21 November 2014, 13:20:10 UTC | Updated `genome` tab completion. | 21 November 2014, 13:20:10 UTC |
1fdf11e | APipe Tester | 21 November 2014, 13:17:06 UTC | Updated class browser cache. | 21 November 2014, 13:17:06 UTC |
2bd9527 | apregier | 21 November 2014, 00:17:37 UTC | Merge pull request #238 from apregier/add_required_experts_docs Add required interpreters and experts section to reporter docs I am merging quickly to try to get this in a snapshot before our presentation tomorrow. | 21 November 2014, 00:17:37 UTC |
4b9e01a | David Morton | 21 November 2014, 00:09:20 UTC | Merge pull request #236 from davidlmorton/process_vr Make VariantReporting::Command::CreateReport use Genome::Process | 21 November 2014, 00:09:20 UTC |
612ab35 | apregier | 21 November 2014, 00:08:28 UTC | Rename methods requires_interpreters and requires_experts | 21 November 2014, 00:08:28 UTC |
d98b23b | apregier | 20 November 2014, 23:26:09 UTC | Add required interpreters and experts section to reporter docs | 20 November 2014, 23:26:09 UTC |
f2f2128 | Adam Coffman | 20 November 2014, 23:23:47 UTC | Merge pull request #237 from acoffman/bless_new_build Bless new test build | 20 November 2014, 23:23:47 UTC |
f25f3c6 | apregier | 20 November 2014, 23:20:52 UTC | Merge pull request #233 from apregier/no_docs_for_transient Don't display transient properties | 20 November 2014, 23:20:52 UTC |
5511601 | Adam Coffman | 20 November 2014, 23:11:20 UTC | bless new test build | 20 November 2014, 23:11:20 UTC |
d321db5 | Eddie Belter | 20 November 2014, 23:10:25 UTC | CgHub: use env genome-perl in test shebang. | 20 November 2014, 23:10:25 UTC |
8000eb7 | apregier | 20 November 2014, 17:47:37 UTC | Don't display transient properties | 20 November 2014, 23:09:20 UTC |
e35c0dc | dmorton | 20 November 2014, 22:43:02 UTC | Update docs | 20 November 2014, 22:43:02 UTC |
cead689 | dmorton | 20 November 2014, 22:32:41 UTC | Make transients optional | 20 November 2014, 22:32:41 UTC |
60022e6 | Feiyu Du | 20 November 2014, 22:16:59 UTC | Modify ExtractReadGroup.pm | 20 November 2014, 22:16:59 UTC |
904de12 | Eddie Belter | 20 November 2014, 21:53:17 UTC | CgHub: move credential file into calculated class property | 20 November 2014, 21:53:17 UTC |
b8e1cf8 | dmorton | 20 November 2014, 21:40:12 UTC | Merge v3 and v4 into v5 test-data | 20 November 2014, 21:40:12 UTC |
083b0cf | dmorton | 20 November 2014, 21:23:46 UTC | Merge branch 'master' of github.com:genome/genome into process_vr Conflicts: lib/perl/Genome/VariantReporting/Suite/Joinx/Homopolymer/Expert.t | 20 November 2014, 21:23:46 UTC |
fdaaf27 | Eddie Belter | 20 November 2014, 21:17:53 UTC | CgHub: add verify success and correct base class to gene torrent; update tests | 20 November 2014, 21:17:53 UTC |
becd9d4 | Susanna Siebert | 20 November 2014, 20:27:54 UTC | Merge pull request #222 from susannasiebert/component_descriptions Add documentation (doc lines) to variant reporting components | 20 November 2014, 20:27:54 UTC |