| 05a7317 | Allison Penner Regier | 06 March 2015, 14:31:26 UTC | Merge pull request #545 from apregier/new_blessed_build PI field is not populated in alignment bams. | 06 March 2015, 14:31:26 UTC |
| de1c402 | apregier | 06 March 2015, 14:28:23 UTC | PI field is not populated in alignment bams. | 06 March 2015, 14:28:23 UTC |
| 579b725 | APipe Tester | 06 March 2015, 13:16:10 UTC | Updated `genome` tab completion. | 06 March 2015, 13:16:10 UTC |
| 9951d24 | APipe Tester | 06 March 2015, 13:14:24 UTC | Updated class browser cache. | 06 March 2015, 13:14:24 UTC |
| b39453e | Thomas B. Mooney | 05 March 2015, 22:07:53 UTC | Merge pull request #536 from tmooney/clinseq_model_test_doesnt_depend_on_prod_database Use the test build to test the ClinSeq file accessors. | 05 March 2015, 22:07:53 UTC |
| 2a8c028 | Thomas B. Mooney | 05 March 2015, 21:40:57 UTC | Merge pull request #534 from tmooney/anp_define_templates New Command to Define an AnalysisProject Template. | 05 March 2015, 21:40:57 UTC |
| 1552c19 | Eddie Belter | 05 March 2015, 17:06:17 UTC | Merge pull request #538 from ebelter/rm-hmp-command InstData: remove unsed hmp command tree | 05 March 2015, 17:06:17 UTC |
| b23bca7 | Eddie Belter | 04 March 2015, 22:38:40 UTC | InstData: remove unsed hmp command tree | 04 March 2015, 22:38:40 UTC |
| 47fe388 | Susanna Siebert | 04 March 2015, 18:53:11 UTC | Merge pull request #537 from tmooney/locking_takes_a_step_back_in_time Revert "Only hash the lock name if we're going to exceed the length limit." | 04 March 2015, 18:53:11 UTC |
| 6ba61ad | Susanna Siebert | 04 March 2015, 16:56:39 UTC | Merge pull request #533 from susannasiebert/library_insert_size Don't populate the PI field | 04 March 2015, 16:56:39 UTC |
| 6d91b1e | Avinash Ramu | 04 March 2015, 16:01:23 UTC | Merge pull request #535 from gatoravi/metadata_export_update Retain build-status in metadata if defined | 04 March 2015, 16:01:23 UTC |
| 30c7196 | Thomas Mooney | 04 March 2015, 15:39:19 UTC | Revert "Only hash the lock name if we're going to exceed the length limit." This reverts commit 1a8c5df57c9de933a8eb555867aa1fc8347a129e. That commit was pretty optimistic about length limits. The exact limit is not knowable in advance, so go back to the probably-fine level of 32 :) A better solution would involve one or more of the following: 1) file locks knowing their own limits in general 2) switching to Nessy :) 3) not storing complex information in labels | 04 March 2015, 15:39:19 UTC |
| 54bb0de | Thomas Mooney | 04 March 2015, 15:13:23 UTC | Use the test build to test the ClinSeq file accessors. | 04 March 2015, 15:13:23 UTC |
| 8d88cf7 | Avinash Ramu | 04 March 2015, 00:11:46 UTC | check for undefined status | 04 March 2015, 00:11:46 UTC |
| 41eec3c | Thomas Mooney | 03 March 2015, 22:26:04 UTC | New command to define a template. | 03 March 2015, 22:26:04 UTC |
| 67cfd1c | Feiyu Du | 03 March 2015, 22:06:49 UTC | update test_db template | 03 March 2015, 22:12:23 UTC |
| daad8de | Thomas B. Mooney | 03 March 2015, 21:56:53 UTC | Merge pull request #529 from tmooney/use_parens_around_list Use parens around list | 03 March 2015, 21:56:53 UTC |
| 9ae144e | Thomas B. Mooney | 03 March 2015, 21:56:44 UTC | Merge pull request #475 from tmooney/private_methods_in_sr_user_locking Tweak internals of SR User locking | 03 March 2015, 21:56:44 UTC |
| 48ca625 | Avinash Ramu | 03 March 2015, 21:43:54 UTC | Retain build status if defined | 03 March 2015, 21:43:54 UTC |
| b997c15 | Susanna Siebert | 02 March 2015, 17:31:13 UTC | Don't populate the PI field | 03 March 2015, 21:43:35 UTC |
| fccf460 | Susanna Siebert | 02 March 2015, 18:51:29 UTC | Some minor cleanup of Bsmap.t | 03 March 2015, 21:43:35 UTC |
| 46e2c19 | Susanna Siebert | 27 February 2015, 21:39:52 UTC | Some minor cleanup of Star.t | 03 March 2015, 21:43:35 UTC |
| ddc1482 | Allison Penner Regier | 03 March 2015, 19:44:56 UTC | Merge pull request #516 from apregier/fix_vep Process needs to be accessible by workflow step | 03 March 2015, 19:44:56 UTC |
| 1915ccf | Thomas Mooney | 02 March 2015, 22:06:18 UTC | Add parens around lists in tests. | 02 March 2015, 22:09:28 UTC |
| 62f769a | Thomas Mooney | 02 March 2015, 22:05:58 UTC | Add parens around lists in GMTs | 02 March 2015, 22:09:28 UTC |
| bdae73c | Thomas Mooney | 02 March 2015, 22:05:39 UTC | Add parens around lists in VariantReporting tests. | 02 March 2015, 22:09:28 UTC |
| 1b6fa5e | Thomas Mooney | 02 March 2015, 22:05:14 UTC | Use parens around lists in VariantReporting. | 02 March 2015, 22:09:28 UTC |
| da73972 | Thomas Mooney | 02 March 2015, 21:42:33 UTC | Add true value at end. | 02 March 2015, 22:07:25 UTC |
| ac997e2 | Thomas Mooney | 02 March 2015, 21:42:15 UTC | Use parens around for-loop list. | 02 March 2015, 22:07:25 UTC |
| 67ac46c | Chris Miller | 02 March 2015, 20:55:57 UTC | Merge pull request #528 from chrisamiller/master Adding reminder that AnPs are created in a Pending state | 02 March 2015, 20:55:57 UTC |
| 1efb0d2 | Nathaniel Nutter | 02 March 2015, 19:03:37 UTC | Merge pull request #522 from nnutter/term try to disable Term::ReadKey warning | 02 March 2015, 19:03:37 UTC |
| b253fe1 | Chris Miller | 02 March 2015, 18:50:52 UTC | adding reminder that projects are created in a Pending state | 02 March 2015, 18:50:52 UTC |
| beec0c4 | Susanna Siebert | 02 March 2015, 17:14:24 UTC | Merge pull request #512 from susannasiebert/variant_reporting_adaptor Remove adaptors from the variant reporting framework | 02 March 2015, 17:14:24 UTC |
| 86d781b | Dave Larson | 02 March 2015, 15:52:32 UTC | Merge pull request #519 from davidlmorton/bam_readcount_vcf_encoding Bam readcount vcf encoding | 02 March 2015, 15:52:32 UTC |
| 11d5189 | Susanna Siebert | 02 March 2015, 15:50:08 UTC | use $class->class | 02 March 2015, 15:50:08 UTC |
| f0c63c8 | Susanna Siebert | 02 March 2015, 15:42:50 UTC | Check for _md5 and _count params on SoftwareResults only | 02 March 2015, 15:42:50 UTC |
| 5c2a585 | Nathaniel Nutter | 01 March 2015, 03:24:13 UTC | Merge pull request #526 from nnutter/test-fixes temporarily disable test | 01 March 2015, 03:24:13 UTC |
| a63bd49 | Nathaniel Nutter | 01 March 2015, 03:12:35 UTC | temporarily disable test See AR-953. | 01 March 2015, 03:12:35 UTC |
| 199d7c5 | Nathaniel Nutter | 28 February 2015, 19:29:03 UTC | disable `warn` using $SIG{__WARN__} | 28 February 2015, 19:58:16 UTC |
| b10f858 | Nathaniel Nutter | 28 February 2015, 19:30:21 UTC | Merge pull request #524 from nnutter/test-db-2 override default timeout when creating an ephemeral database | 28 February 2015, 19:30:21 UTC |
| c6d1658 | Nathaniel Nutter | 28 February 2015, 19:09:58 UTC | override default timeout when creating an ephemeral database We've had these errors every once in awhile, > Got error response 500: SSL read timeout: at > /usr/bin/test-db-database-create line 15 Previously we added the `--timeout` option but we didn't think it should be necessary. Now I am thinking it may be that the template locks while creating the new database so contention is what is causing the timeouts. For now I am just increasing the timeout as a workaround. We'll need to see if this is actually what's going on. | 28 February 2015, 19:09:58 UTC |
| 7c8eae3 | dmorton | 28 February 2015, 16:30:13 UTC | Update test data | 28 February 2015, 16:30:13 UTC |
| 5283fe9 | Nathaniel Nutter | 28 February 2015, 05:33:11 UTC | Merge pull request #523 from nnutter/test-fixes fixes for tests that broke when apipe-tester config changed | 28 February 2015, 05:33:11 UTC |
| 9d79843 | Nathaniel Nutter | 28 February 2015, 03:49:13 UTC | fixes for tests that broke when apipe-tester config changed These tests broke when we change apipe-tester's config to use the "pd" queues. | 28 February 2015, 03:49:13 UTC |
| b8c085e | dmorton | 27 February 2015, 22:37:10 UTC | Fix missing " | 27 February 2015, 22:37:10 UTC |
| f9f8854 | APipe Tester | 27 February 2015, 22:18:48 UTC | updated jenkins submodule to da87b38 | 27 February 2015, 22:18:56 UTC |
| f61f7c1 | Nathaniel Nutter | 27 February 2015, 22:18:49 UTC | Merge pull request #520 from acoffman/update_test_db_template Update test db snapshot version | 27 February 2015, 22:18:49 UTC |
| 38ce8d6 | Nathaniel Nutter | 27 February 2015, 22:11:44 UTC | Merge pull request #521 from nnutter/typo fix typo | 27 February 2015, 22:11:44 UTC |
| 5c70819 | Nathaniel Nutter | 27 February 2015, 21:56:58 UTC | try to disable Term::ReadKey warning I don't know of a way to test this easily so I don't know that this works. I'm trying to disable the warnings that shows up on apipe-ci logs, > 13:40:44 Unable to get Terminal Size. The TIOCGWINSZ ioctl didn't > work. The COLUMNS and LINES environment variables didn't work. The > resize program didn't work. at /usr/lib/perl5/Term/ReadKey.pm line > 362. | 27 February 2015, 21:56:58 UTC |
| 4d74968 | Nathaniel Nutter | 27 February 2015, 21:53:06 UTC | fix typo | 27 February 2015, 21:53:06 UTC |
| 625e64c | Adam Coffman | 27 February 2015, 21:43:01 UTC | Update test db snapshot version This includes the missing ClinSeq test build | 27 February 2015, 21:43:01 UTC |
| 932e15e | dmorton | 27 February 2015, 19:51:32 UTC | Correct the header field | 27 February 2015, 19:51:32 UTC |
| 415bcf3 | dmorton | 27 February 2015, 19:50:30 UTC | Swap out , characters for vcf spec compatibility The json encoding introduces both : and , characters which violate the vcf field specification | 27 February 2015, 19:50:30 UTC |
| d5ccdac | dmorton | 27 February 2015, 19:48:36 UTC | Remove swap for \t The json spec disallows tab characters in json strings and so the json library already takes care of these for us. | 27 February 2015, 19:48:36 UTC |
| eb3d990 | Nathaniel Nutter | 27 February 2015, 19:04:57 UTC | Merge pull request #518 from nnutter/test-db promote genome-*env-next | 27 February 2015, 19:04:57 UTC |
| f734ace | Jim Weible | 27 February 2015, 18:04:37 UTC | Merge pull request #505 from jweible/AUE-377 Restrict AnalysisMenu Item Create | 27 February 2015, 18:04:37 UTC |
| 5691095 | Susanna Siebert | 27 February 2015, 15:59:15 UTC | Merge pull request #515 from susannasiebert/variant_reporting_merge_reports Split entry_sources of MergeReports into base_report_source and supplemental_report_source | 27 February 2015, 15:59:15 UTC |
| f746ba2 | Susanna Siebert | 27 February 2015, 14:43:15 UTC | replace erroneous , with ; | 27 February 2015, 14:43:35 UTC |
| fde810b | Susanna Siebert | 27 February 2015, 14:42:54 UTC | add `defined` where appropriate | 27 February 2015, 14:42:54 UTC |
| e88a61d | APipe Tester | 26 February 2015, 23:04:36 UTC | updated ur submodule to 74df78e | 26 February 2015, 23:04:36 UTC |
| 07a3d3c | Nathaniel Nutter | 26 February 2015, 22:43:27 UTC | replace `genome-env-next` with `genome-env` | 26 February 2015, 22:43:27 UTC |
| 3dbd66a | Nathaniel Nutter | 26 February 2015, 22:42:37 UTC | remove debug statements | 26 February 2015, 22:42:37 UTC |
| 9d1453e | Nathaniel Nutter | 26 February 2015, 22:40:22 UTC | symlink genome-*-next back in to ease transition | 26 February 2015, 22:40:22 UTC |
| 59aad14 | Nathaniel Nutter | 26 February 2015, 22:39:10 UTC | "promote" the genome-env-next to genome-env | 26 February 2015, 22:39:10 UTC |
| eddd1ed | Thomas B. Mooney | 26 February 2015, 21:38:02 UTC | Merge pull request #514 from tmooney/sr_user_locking_improvements More SR User Locking Improvements | 26 February 2015, 21:38:02 UTC |
| 7677bf1 | Thomas B. Mooney | 26 February 2015, 21:19:34 UTC | Merge pull request #517 from tmooney/disable_auto_assign_inst_data Disable auto_assign_inst_data as a feature for now. | 26 February 2015, 21:19:34 UTC |
| f1f2035 | Susanna Siebert | 26 February 2015, 21:16:38 UTC | Deletion of special hash keys isn't needed anymore | 26 February 2015, 21:16:38 UTC |
| 155aa24 | Susanna Siebert | 26 February 2015, 21:01:04 UTC | remove is_argument attributes_have and instead get properties from result_class | 26 February 2015, 21:14:14 UTC |
| eeadfb2 | Susanna Siebert | 26 February 2015, 20:00:34 UTC | remove unneeded attributes_have | 26 February 2015, 21:02:05 UTC |
| a2c2c29 | Susanna Siebert | 26 February 2015, 19:32:47 UTC | remove unneeded for-loops | 26 February 2015, 21:02:05 UTC |
| 1a8c5df | Thomas Mooney | 26 February 2015, 20:49:42 UTC | Only hash the lock name if we're going to exceed the length limit. This preserves compatbility with all existing locks while allowing new ones to work. | 26 February 2015, 20:49:42 UTC |
| ee74d64 | Thomas Mooney | 26 February 2015, 19:55:34 UTC | Disable auto_assign_inst_data as a feature for now. | 26 February 2015, 19:55:34 UTC |
| fedf505 | apregier | 26 February 2015, 19:41:35 UTC | Use perl's build in local functionality | 26 February 2015, 19:41:35 UTC |
| a43ec55 | apregier | 26 February 2015, 19:32:20 UTC | Process needs to be accessible by workflow step The process hasn't been committed yet, so shelling out for the workflow steps will fail. By setting NO_LSF, the workflow will be run in the same context and the process will be accessible. | 26 February 2015, 19:32:20 UTC |
| 94d5aa0 | Susanna Siebert | 26 February 2015, 17:55:39 UTC | add report sources for discovery/followup reports | 26 February 2015, 17:55:39 UTC |
| 9eb958c | Susanna Siebert | 26 February 2015, 16:25:04 UTC | split entry_sources into base_report_source and supplemental_report_source | 26 February 2015, 16:25:04 UTC |
| d02a78d | APipe Tester | 26 February 2015, 13:17:46 UTC | Updated `genome` tab completion. | 26 February 2015, 13:17:46 UTC |
| 1a74435 | Thomas Mooney | 25 February 2015, 23:48:34 UTC | Use the unhashed lock name if the label is shorter. | 25 February 2015, 23:48:34 UTC |
| a0ffec5 | Avinash Ramu | 25 February 2015, 23:35:10 UTC | Merge pull request #456 from gatoravi/docm-update clin-seq docm report update | 25 February 2015, 23:35:10 UTC |
| 2d9caf3 | Nathaniel Nutter | 25 February 2015, 23:34:47 UTC | Merge pull request #513 from nnutter/test-db-2 updated to template with 5.10-reference-alignment-lane-qc data | 25 February 2015, 23:34:47 UTC |
| 8b8ea6d | Nathaniel Nutter | 25 February 2015, 23:34:36 UTC | Merge pull request #511 from nnutter/test-db improvements to genome-env-tests | 25 February 2015, 23:34:36 UTC |
| e5d79e9 | Thomas Mooney | 25 February 2015, 21:52:27 UTC | MD5 the label since they sometime get really long. | 25 February 2015, 22:24:20 UTC |
| e2cb1e0 | Thomas Mooney | 25 February 2015, 21:50:07 UTC | Use new "once" property of observers to simplify callbacks. | 25 February 2015, 22:24:20 UTC |
| a1dbf28 | Susanna Siebert | 25 February 2015, 21:59:44 UTC | Fix one type that was missed in last commit | 25 February 2015, 21:59:44 UTC |
| 3407614 | Susanna Siebert | 25 February 2015, 21:57:11 UTC | Fix docs and types or runners to match past adaptor, where appropriate | 25 February 2015, 21:57:11 UTC |
| ce345bd | Susanna Siebert | 25 February 2015, 21:47:32 UTC | Make lsf_resource is_structural | 25 February 2015, 21:47:32 UTC |
| 8ec2f1c | Susanna Siebert | 25 February 2015, 21:21:20 UTC | Handle _count params in a special way - With the removal of adaptors certain arguments have become is_param. If one of them is named _count it will be filtered out and not displayed in the docs. The paras that we want to actually filter out are related to is_many software result params. These have a _count and a _md5 equivalent. We use this to only filter out _count params if there is a matching _md5 param. | 25 February 2015, 21:21:20 UTC |
| 33f7bab | Susanna Siebert | 25 February 2015, 20:48:00 UTC | Set expert requestor to is_structural so it doesn't appear in docs | 25 February 2015, 21:20:52 UTC |
| 33df36b | Susanna Siebert | 25 February 2015, 20:39:55 UTC | Set expert inputs and outputs to is_structural so they don't appear in docs | 25 February 2015, 21:20:51 UTC |
| 5627899 | Eddie Belter | 25 February 2015, 20:50:26 UTC | Merge pull request #503 from ebelter/flexbar InstData Solexa: fix param read trimmer param parsing | 25 February 2015, 20:50:26 UTC |
| b949575 | Nathaniel Nutter | 25 February 2015, 19:51:16 UTC | updated to template with 5.10-reference-alignment-lane-qc data | 25 February 2015, 19:51:16 UTC |
| 479b503 | Allison Penner Regier | 25 February 2015, 19:34:14 UTC | Merge pull request #508 from apregier/add_process_diff_tests Add process diff tests | 25 February 2015, 19:34:14 UTC |
| ee4b10a | APipe Tester | 25 February 2015, 18:56:32 UTC | Updated `genome` tab completion. | 25 February 2015, 18:56:32 UTC |
| f699c76 | APipe Tester | 25 February 2015, 18:54:16 UTC | Updated class browser cache. | 25 February 2015, 18:54:16 UTC |
| 9aaa405 | Susanna Siebert | 25 February 2015, 18:32:21 UTC | Update show-docs | 25 February 2015, 18:32:21 UTC |
| e91184a | Susanna Siebert | 25 February 2015, 16:30:48 UTC | Change expert command test to work without adaptor and add previous adaptor tests | 25 February 2015, 18:31:34 UTC |
| 857cec5 | Susanna Siebert | 25 February 2015, 15:26:40 UTC | Update expected xml test files | 25 February 2015, 18:31:34 UTC |
| 9a1b8f6 | Susanna Siebert | 25 February 2015, 15:26:16 UTC | Fix test plan files for is_many input | 25 February 2015, 18:31:34 UTC |
| 1f509cc | Susanna Siebert | 25 February 2015, 15:25:45 UTC | Change test experts to work without adaptor | 25 February 2015, 18:31:34 UTC |
| 2f2d8ed | Susanna Siebert | 25 February 2015, 15:22:38 UTC | Include is_many inputs in needed_translations | 25 February 2015, 18:31:33 UTC |
