| 3262ca7 | David Morton | 17 March 2015, 14:55:54 UTC | Merge pull request #564 from dufeiyu/bug_fix Make Htseq count to revivify the per lane bam from merged bam | 17 March 2015, 14:55:54 UTC |
| 3459f61 | Nathaniel Nutter | 16 March 2015, 23:20:21 UTC | Merge pull request #559 from nnutter/RT-104532 support importing "new" Nimblegen capture/primary split bed files | 16 March 2015, 23:20:21 UTC |
| e260743 | Jason Walker | 16 March 2015, 20:01:23 UTC | Merge pull request #558 from jasonwalker80/de_optional_cummerbund DE - cummeRbund optional | 16 March 2015, 20:01:23 UTC |
| 1f488c1 | Nathaniel Nutter | 16 March 2015, 19:08:29 UTC | remove use of capture/primary in names | 16 March 2015, 19:13:47 UTC |
| b3cbed6 | Nathaniel Nutter | 16 March 2015, 19:01:58 UTC | remove chromosome name "fixing" code | 16 March 2015, 19:01:58 UTC |
| a5ba4de | Nathaniel Nutter | 16 March 2015, 19:00:14 UTC | remove description since FeatureList ignores it anyway | 16 March 2015, 19:00:14 UTC |
| 33c1a43 | Anthony Brummett | 16 March 2015, 14:41:53 UTC | Merge pull request #562 from brummett/error-message Avoid an additional error when we can't connect to the logging DB | 16 March 2015, 14:41:53 UTC |
| 9420883 | Anthony Brummett | 16 March 2015, 14:41:15 UTC | Merge pull request #561 from brummett/datetime Fix DateTime calculation involving DST | 16 March 2015, 14:41:15 UTC |
| 1b55686 | Susanna Siebert | 16 March 2015, 14:03:55 UTC | Merge pull request #563 from susannasiebert/picard_help_detail Fix help_detail links to point to correct anchor | 16 March 2015, 14:03:55 UTC |
| c9c90cb | Thomas B. Mooney | 16 March 2015, 13:47:55 UTC | Merge pull request #549 from tmooney/cqid_queries_undef_properties CQID: Only filter undef properties from model creation. | 16 March 2015, 13:47:55 UTC |
| 5cf6f2c | APipe Tester | 14 March 2015, 21:17:56 UTC | updated ur submodule to 7e7d60a | 14 March 2015, 21:17:56 UTC |
| a2a3da9 | Feiyu Du | 14 March 2015, 20:39:47 UTC | bugfix 1. make Htseq count to revivify the per lane bam from merged bam 2. input correct instrument_data_id to RecreatePerLaneBam | 14 March 2015, 20:39:47 UTC |
| f75c3f1 | APipe Tester | 14 March 2015, 00:27:39 UTC | updated jenkins submodule to e661237 | 14 March 2015, 00:27:39 UTC |
| 512735f | Susanna Siebert | 13 March 2015, 18:30:03 UTC | fix help_detail links to point to correct anchor | 13 March 2015, 18:30:03 UTC |
| e62bed3 | Nathaniel Nutter | 13 March 2015, 18:22:31 UTC | use open_file_for_reading instead of IO::File Use `open_file_for_reading` instead of `IO::File->new` to get "free" validation that file was opened for reading. | 13 March 2015, 18:22:31 UTC |
| 448cf32 | Nathaniel Nutter | 13 March 2015, 18:19:25 UTC | pass around a hash instead of an array Using a hash is a more explicit than relying on the position in the array (with or without sorting). | 13 March 2015, 18:19:25 UTC |
| 787cb6f | Nathaniel Nutter | 13 March 2015, 18:11:09 UTC | use try instead of eval for proper scoping of $@ | 13 March 2015, 18:11:09 UTC |
| 9f9bd8d | Anthony Brummett | 13 March 2015, 17:15:53 UTC | Avoid an additional error when we can't connect to the logging DB The PostgreSQL error message can contain the server name in double quotes, which messes up building the string to be eval-ed, which generates an error about a runaway string. This escapes those quotes. | 13 March 2015, 17:15:53 UTC |
| 83865e2 | Anthony Brummett | 13 March 2015, 14:34:00 UTC | Fix DateTime calculation involving DST Builds were failing on Mar 13 between 2 and 3AM. _default_archive_after_time() adds 1 year to the current time. The 2016 DST changeover will happen on Mar 13, so 13 Mar 2016 2:45:00 won't exist. The error would also occur for any allocations created on Feb 29th. This change adds an equivalent number of seconds, which DateTime allows, and automatically adjusts for time changes. One downside is that when there's a Feb 29th between "now" and the calculated date, you'll technically have 1 day less than a year before it's archived. The alternative is to use DateTime's "floating" timezone (https://metacpan.org/pod/DateTime#Making-Things-Simple) which allows the calculation to produce an invalid date in the local timezone, but this seems more hacky. | 13 March 2015, 14:34:00 UTC |
| 73b488f | APipe Tester | 13 March 2015, 12:18:45 UTC | Updated `gmt` tab completion. | 13 March 2015, 12:18:45 UTC |
| 4ffb7e9 | APipe Tester | 13 March 2015, 12:17:57 UTC | Updated `genome` tab completion. | 13 March 2015, 12:17:57 UTC |
| d960702 | APipe Tester | 13 March 2015, 12:16:13 UTC | Updated class browser cache. | 13 March 2015, 12:16:13 UTC |
| d1de83c | Nathaniel Nutter | 12 March 2015, 23:15:54 UTC | fix typo | 12 March 2015, 23:15:54 UTC |
| 0c072db | Nathaniel Nutter | 12 March 2015, 23:13:03 UTC | support importing "new" Nimblegen capture/primary split bed files Add support for importing Nimblegen capture_targets/primary_targets split bed files. This feature was requested in [RT#104532][1]. [1]: https://rt.gsc.wustl.edu/Ticket/Display.html?id=104532 | 12 March 2015, 23:13:03 UTC |
| 48d7c2f | Allison Penner Regier | 12 March 2015, 21:16:03 UTC | Merge pull request #502 from tabbott/picard-refactor Picard refactoring | 12 March 2015, 21:16:03 UTC |
| d11a9d5 | Feiyu Du | 12 March 2015, 19:48:02 UTC | Merge pull request #407 from gsanders/recreate_per_lane_bam Recreate per-lane bams on demand (and delete them when done) | 12 March 2015, 19:48:02 UTC |
| daf800d | Jason Walker | 12 March 2015, 18:21:48 UTC | Make cummerbund an optional part of the workflow. | 12 March 2015, 18:21:48 UTC |
| 587ff67 | Eddie Belter | 11 March 2015, 19:53:56 UTC | Merge pull request #553 from ebelter/genotype-concordance-users GMT Genotype CC: add users to VCF result | 11 March 2015, 19:53:56 UTC |
| 7ea4a62 | Eddie Belter | 11 March 2015, 19:47:22 UTC | Merge pull request #551 from ebelter/allpaths Allpaths: sanitize library names befroe writing to csv | 11 March 2015, 19:47:22 UTC |
| 57b6448 | Gabriel Sanderson | 11 March 2015, 18:50:48 UTC | pluralize _lock_per_lane_alignment | 11 March 2015, 18:50:48 UTC |
| 9d22a6d | Susanna Siebert | 11 March 2015, 17:28:29 UTC | Merge pull request #550 from susannasiebert/variant_reporting_vep CHANGELOG: Add option to variant reporting vep expert to use use short_name instead of name column in feature list. This keep the vep expert from failing if a feature list contains a special character, like semicolons. short_name is a required parameter so if your variant reporting plan file uses the vep expert you will need to add `short_name: 0` to the list of vep expert parameters. If you want to turn on the short_name option your need to add `short_name: 1` to the list of vep expert parameters. | 11 March 2015, 17:28:29 UTC |
| 51c00a1 | mkiwala | 11 March 2015, 17:15:29 UTC | Merge pull request #463 from mkiwala/update-determine-error Recognize new date format | 11 March 2015, 17:15:29 UTC |
| bd4ec3a | Nathaniel Nutter | 11 March 2015, 16:45:35 UTC | Merge pull request #554 from nnutter/test-fixes possible fix for apipe-ci/bats test failures | 11 March 2015, 16:45:35 UTC |
| cca6723 | Avinash Ramu | 11 March 2015, 16:18:18 UTC | Merge pull request #552 from gatoravi/site_sgms add site config for SGMS | 11 March 2015, 16:18:18 UTC |
| 188fe46 | Thomas B. Mooney | 11 March 2015, 15:35:18 UTC | Merge pull request #555 from tmooney/strip_priority_from_host_group Strip priorities from host-group parsing. | 11 March 2015, 15:35:18 UTC |
| 0cc1e8b | Thomas Mooney | 11 March 2015, 15:12:33 UTC | Strip priorities from host-group parsing. | 11 March 2015, 15:12:33 UTC |
| 3d5182c | Nathaniel Nutter | 11 March 2015, 05:54:23 UTC | possible fix for apipe-ci/bats test failures We've previously seen errors like this: (from function `cache_repo' in file test_helper.bash, line 34, from function `init_workspace' in file test_helper.bash, line 44, from function `setup' in test file submodule.bats, line 6) `init_workspace' failed with status 128 At the time Tom said he nuked the directories to fix it. The Git repos are being corrupted and I suspect it's because `tmpreaper` is trying to clean up. | 11 March 2015, 05:54:23 UTC |
| 2ef64da | Gabriel Sanderson | 10 March 2015, 22:30:28 UTC | Updated comment - we aren't avoiding NO_COMMIT in the code any longer. | 10 March 2015, 22:30:28 UTC |
| 45d7fa6 | Gabriel Sanderson | 10 March 2015, 22:04:40 UTC | Do not remove per-lane bam files with NO_COMMIT on. | 10 March 2015, 22:04:40 UTC |
| 681091c | Avinash Ramu | 10 March 2015, 21:56:48 UTC | specify right module | 10 March 2015, 21:56:48 UTC |
| b5acbd1 | Gabriel Sanderson | 10 March 2015, 21:47:12 UTC | Remove duplicate logic - resize_disk_allocation method. | 10 March 2015, 21:47:12 UTC |
| 287033b | Gabriel Sanderson | 10 March 2015, 21:20:11 UTC | Minor code review adjustments | 10 March 2015, 21:20:11 UTC |
| 6dcc9ae | Eddie Belter | 10 March 2015, 17:55:33 UTC | Allpaths: sanitize lib name w/ sanitize_for_filesystem | 10 March 2015, 17:55:33 UTC |
| 45ac622 | Allison Penner Regier | 10 March 2015, 16:19:40 UTC | Merge pull request #540 from apregier/new_genome-env_option New genome-env option | 10 March 2015, 16:19:40 UTC |
| 51e7916 | Susanna Siebert | 10 March 2015, 15:39:31 UTC | Only validate feature lists of short_name option is not set | 10 March 2015, 15:39:31 UTC |
| 2f1ac6c | Susanna Siebert | 10 March 2015, 15:38:38 UTC | Update error message to mention the short_name option | 10 March 2015, 15:38:38 UTC |
| a4c2fdb | Susanna Siebert | 10 March 2015, 15:34:53 UTC | check the first 100 lines, instead of just 10 | 10 March 2015, 15:34:53 UTC |
| d3b2a71 | Susanna Siebert | 10 March 2015, 15:33:50 UTC | Revert "remove feature list validation" This reverts commit 7d071a76e4bc62b5d2cb69f2dc4270a5eb4b1992. | 10 March 2015, 15:33:50 UTC |
| 914bc8f | Avinash Ramu | 10 March 2015, 04:58:38 UTC | add site config for SGMS | 10 March 2015, 04:58:38 UTC |
| 4795208 | Eddie Belter | 10 March 2015, 00:10:51 UTC | GMT Genotype CC: send qc build as sponsor/requestor to VCF result | 10 March 2015, 00:44:39 UTC |
| 69d594b | Eddie Belter | 10 March 2015, 00:10:24 UTC | GMT Genotype CC: update to __display_name__ | 10 March 2015, 00:10:24 UTC |
| f4e45b7 | Eddie Belter | 09 March 2015, 22:56:40 UTC | Allpaths: sanitize library names befroe writing to csv | 09 March 2015, 22:56:40 UTC |
| 79ca349 | Malachi Griffith | 09 March 2015, 22:38:40 UTC | Merge pull request #548 from malachig/master ClinSeq: update analysis now specifies cancer, misc, cosmic DBs | 09 March 2015, 22:38:40 UTC |
| b09e161 | Gabriel Sanderson | 09 March 2015, 22:05:53 UTC | Corrected lock location (no absolute paths) | 09 March 2015, 22:05:53 UTC |
| 7d071a7 | Susanna Siebert | 09 March 2015, 16:01:26 UTC | remove feature list validation | 09 March 2015, 21:54:45 UTC |
| 2fd4db5 | Susanna Siebert | 09 March 2015, 16:01:00 UTC | add option to vep expert to use short_name option in Genome::FeatureList::processed_bed_file_content | 09 March 2015, 21:54:45 UTC |
| 55e1ac0 | Malachi Griffith | 09 March 2015, 21:06:44 UTC | clin-seq: remove redundant use of default db id values and rename some variables for clarity | 09 March 2015, 21:06:44 UTC |
| 0955c4a | apregier | 09 March 2015, 20:32:19 UTC | Host and port will always come from either -i or test-db | 09 March 2015, 20:32:19 UTC |
| e3f9505 | apregier | 09 March 2015, 20:31:46 UTC | Always print host and port | 09 March 2015, 20:31:46 UTC |
| 5a70067 | Thomas Mooney | 09 March 2015, 18:32:54 UTC | Only filter undef properties from model creation. Omitting "undef" from the get() queries may pull back non-matching models, but including "undef" in create() calls may generate invalid hangoff objects. | 09 March 2015, 18:32:54 UTC |
| 5c14d3a | apregier | 09 March 2015, 17:23:59 UTC | Add an option to not delete db when the shell goes away | 09 March 2015, 17:23:59 UTC |
| 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 |
| ff7269a | Gabriel Sanderson | 07 March 2015, 00:04:46 UTC | Rename recreated->revivified for consistency. | 07 March 2015, 00:04:46 UTC |
| d354b39 | Gabriel Sanderson | 06 March 2015, 23:52:39 UTC | Prefer recreating per-lane bams to using them in-place. Cache the path. This fixes two things: 1) Prefering to recreate files, rather than using the in-place file allows us to run a clean-up script much more easily. With this code we can now delete all existing per-lane bam files that already have merged alignment results, without interfering with any current merge processes. This will save us from forcing an alignment queue downtime when we clean up and backfill after this is merged. 2) Caching the path prevents us from recreating many files for the same per-lane alignment result object instance, when we've already done it. | 06 March 2015, 23:52:39 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 |
| db1d980 | Malachi Griffith | 06 March 2015, 22:06:30 UTC | ClinSeq: update analysis now specifies cancer, misc, cosmic DBs in clin-seq model define commands when a non-default version is specified by the user | 06 March 2015, 22:06:30 UTC |
| c170675 | Gabriel Sanderson | 06 March 2015, 21:45:14 UTC | Do not care about UR_DBI_NO_COMMIT, locking does the right thing. | 06 March 2015, 21:45:14 UTC |
| ff04821 | Gabriel Sanderson | 06 March 2015, 21:31:25 UTC | Refactor testing logic into unit tests and away from real code. More of the same. | 06 March 2015, 21:31:25 UTC |
| 3e02b78 | Gabriel Sanderson | 06 March 2015, 21:20:34 UTC | Refactor testing logic into unit tests and away from real code. | 06 March 2015, 21:20:34 UTC |
| 9491216 | Gabriel Sanderson | 06 March 2015, 21:13:05 UTC | Size up allocation for extra files. Remove bam with commit hook instead. | 06 March 2015, 21:13:05 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 |
| 7cf9df3 | Gabriel Sanderson | 05 March 2015, 20:33:00 UTC | Workaround for new software result user relationships | 05 March 2015, 20:33:00 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 |
| e03b85b | apregier | 05 March 2015, 18:09:36 UTC | Fix help message | 05 March 2015, 18:10:18 UTC |
| 95462bb | apregier | 05 March 2015, 18:08:28 UTC | Add -i option for creating an environment from an existing db | 05 March 2015, 18:10:17 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 |
| 76c85bb | Gabriel Sanderson | 05 March 2015, 03:58:34 UTC | Correct call to collect_individual_alignments. Clean up. | 05 March 2015, 03:58:34 UTC |
| b23bca7 | Eddie Belter | 04 March 2015, 22:38:40 UTC | InstData: remove unsed hmp command tree | 04 March 2015, 22:38:40 UTC |
