| 7e4b64d | Susanna Siebert | 09 March 2015, 14:23:48 UTC | Merge pull request #543 from susannasiebert/variant_reporting_vaf Variant reporting vaf interpreter bugfix | 09 March 2015, 14:23:48 UTC |
| 7908975 | Thomas B. Mooney | 09 March 2015, 13:18:30 UTC | Merge pull request #539 from tmooney/queueing_for_everyone No longer hide build queue in docs. | 09 March 2015, 13:18:30 UTC |
| e3cd42b | Thomas B. Mooney | 09 March 2015, 13:18:18 UTC | Merge pull request #544 from tmooney/microarray_vcf_result_respects_create_semantics SUPER::create() may return undef--pass it along. | 09 March 2015, 13:18:18 UTC |
| f68f4c4 | APipe Tester | 07 March 2015, 13:17:25 UTC | Updated `gmt` tab completion. | 07 March 2015, 13:17:25 UTC |
| 130dae9 | APipe Tester | 07 March 2015, 13:16:39 UTC | Updated `genome` tab completion. | 07 March 2015, 13:16:39 UTC |
| 83f5b0f | David Morton | 07 March 2015, 00:47:31 UTC | Merge pull request #541 from davidlmorton/park_beta_move Park beta move | 07 March 2015, 00:47:31 UTC |
| 7f1c129 | David Morton | 07 March 2015, 00:47:17 UTC | Merge pull request #542 from davidlmorton/dindel-ccsvcf Add max_haplotypes as option for ccsvcf for indels | 07 March 2015, 00:47:17 UTC |
| 763ec02 | Eddie Belter | 06 March 2015, 22:54:18 UTC | Merge pull request #532 from ebelter/stdout-fh Sys: Do not close the fh in write_file if writing to STDOUT | 06 March 2015, 22:54:18 UTC |
| 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 |
| 8e0d631 | dmorton | 05 March 2015, 22:40:09 UTC | Update test-data for ccsvcf indels | 05 March 2015, 22:40:09 UTC |
| c6873ec | Thomas Mooney | 05 March 2015, 22:30:19 UTC | SUPER::create() may return undef--pass it along. get_or_create() will then try to get() one last time (if create detected that the object was made already). Crashing prevents this from working. | 05 March 2015, 22:30:19 UTC |
| 7c1c233 | Susanna Siebert | 05 March 2015, 22:10:37 UTC | Use next instead of erroneous return | 05 March 2015, 22:10:37 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 |
| 9e0857b | Susanna Siebert | 05 March 2015, 21:28:07 UTC | remove production sample names from long indel test and vcf | 05 March 2015, 21:28:07 UTC |
| 2be875c | Susanna Siebert | 05 March 2015, 21:21:46 UTC | remove unneeded available_libraries | 05 March 2015, 21:21:46 UTC |
| e5e0d82 | dmorton | 05 March 2015, 21:10:34 UTC | Add max_haplotypes option to ccsvcf for indels | 05 March 2015, 21:14:30 UTC |
| e234e8b | dmorton | 05 March 2015, 20:41:21 UTC | Organize the inputs tsv file | 05 March 2015, 21:14:18 UTC |
| 1d658b0 | Susanna Siebert | 05 March 2015, 20:47:56 UTC | stop flatten_hash from stomping on its previous executions | 05 March 2015, 20:47:56 UTC |
| 3995863 | Susanna Siebert | 05 March 2015, 19:53:36 UTC | fix interpretation null character return values to include the correct fields | 05 March 2015, 20:16:18 UTC |
| 7e3bd0a | dmorton | 05 March 2015, 20:16:06 UTC | Move ParkBeta to disk that isn't full | 05 March 2015, 20:16:06 UTC |
| 34bf378 | dmorton | 05 March 2015, 20:15:06 UTC | Make GENOME_PARK_BETA_ROOT env variable | 05 March 2015, 20:15:06 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 |
| 6ad54b3 | Thomas Mooney | 05 March 2015, 16:02:29 UTC | No longer hide build queue in docs. | 05 March 2015, 16:02:29 UTC |
| b23bca7 | Eddie Belter | 04 March 2015, 22:38:40 UTC | InstData: remove unsed hmp command tree | 04 March 2015, 22:38:40 UTC |
| c9689c3 | Eddie Belter | 04 March 2015, 21:20:10 UTC | Sys: remove use Test::Exception | 04 March 2015, 21:20:10 UTC |
| 5abbfc0 | Eddie Belter | 04 March 2015, 21:18:57 UTC | Sys: remove select statement | 04 March 2015, 21:18:57 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 |
| 4b5e1c1 | Eddie Belter | 03 March 2015, 21:32:59 UTC | Sys: skip closing FH in write file when writingto STDOUT | 03 March 2015, 21:32:59 UTC |
| 60cc088 | Eddie Belter | 03 March 2015, 20:49:46 UTC | Sys: add test showing writing to STDOUT twice via write_file fails | 03 March 2015, 20:49:46 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 |
