| 56ba285 | APipe Tester | 01 May 2015, 06:36:18 UTC | updated ur submodule to ee4eea5 | 01 May 2015, 06:36:18 UTC |
| e0210b7 | Nathaniel Nutter | 01 May 2015, 06:19:07 UTC | Merge pull request #709 from nnutter/try remove `local $@` | 01 May 2015, 06:19:07 UTC |
| 6dea2ee | dmorton | 01 May 2015, 02:44:27 UTC | Encode inputs before submitting | 01 May 2015, 02:44:27 UTC |
| 5473517 | Ian Ferguson | 30 April 2015, 22:34:03 UTC | Merge pull request #706 from davidlmorton/processes_without_workflow_slot PTero can run Processes without a workflow slot | 30 April 2015, 22:34:03 UTC |
| 04ecd0a | Nathaniel Nutter | 30 April 2015, 20:04:32 UTC | Merge pull request #705 from nnutter/master show stderr when trying to load module for assert_module_found | 30 April 2015, 20:04:32 UTC |
| 0278f05 | Thomas B. Mooney | 30 April 2015, 19:53:22 UTC | Merge pull request #704 from tmooney/remove_skipped_refcov_code Remove Long-Skipped RefCov Code | 30 April 2015, 19:53:22 UTC |
| af8420a | dmorton | 30 April 2015, 18:59:45 UTC | Ensure undef environment doesn't get into json. | 30 April 2015, 18:59:45 UTC |
| 41b6299 | Thomas B. Mooney | 30 April 2015, 18:26:54 UTC | Merge pull request #703 from tmooney/open_fewer_filehandles_in_alignment_summary Open fewer simultaneous filehandles in AlignmentSummaryV2 | 30 April 2015, 18:26:54 UTC |
| 0ee2b0b | Thomas B. Mooney | 30 April 2015, 18:25:32 UTC | Merge pull request #701 from tmooney/more_memory_for_fastqc Bump FastQC's JVM memory request to 512 MB. | 30 April 2015, 18:25:32 UTC |
| cc71768 | dmorton | 30 April 2015, 17:02:30 UTC | Make VALID_STATUS_VALUES a function | 30 April 2015, 17:02:30 UTC |
| 242ea19 | dmorton | 30 April 2015, 16:56:16 UTC | Fix capitalization | 30 April 2015, 16:56:16 UTC |
| bd3630d | Thomas B. Mooney | 30 April 2015, 13:05:00 UTC | Merge pull request #700 from tmooney/use_official_merged_result_in_somval_identifydnp Use the labelled merged result in SomaticValidation's Identify DNP | 30 April 2015, 13:05:00 UTC |
| cec29fb | dmorton | 30 April 2015, 02:29:58 UTC | Update test data after change to output name. | 30 April 2015, 02:29:58 UTC |
| 3af2619 | Nathaniel Nutter | 29 April 2015, 22:29:46 UTC | replace use of `local $@` by using `exception` | 29 April 2015, 22:29:46 UTC |
| 383b7c8 | Nathaniel Nutter | 29 April 2015, 22:24:41 UTC | replace use of `local $@` by removing `eval` If we want to test something didn't die just don't catch it. | 29 April 2015, 22:29:28 UTC |
| 078ee54 | Nathaniel Nutter | 29 April 2015, 22:23:05 UTC | remove unnecessary `local $@` There used to be an `eval` on the line after but the `eval` was removed and the `local $@` was not. | 29 April 2015, 22:23:05 UTC |
| f5a66d0 | Nathaniel Nutter | 29 April 2015, 22:22:13 UTC | preserve value of `$@` If something in `$self->delete` used an `eval` then `$@` would be cleared. | 29 April 2015, 22:22:13 UTC |
| 626f262 | Nathaniel Nutter | 29 April 2015, 22:20:36 UTC | localizing $@ can suppress error message If `$transaction->rollback` threw an exception and a caller caught it then `$@` would not be set due to `local $@`. | 29 April 2015, 22:20:36 UTC |
| af52f2b | dmorton | 27 April 2015, 00:24:48 UTC | Can now see notes with 'genome process view' | 29 April 2015, 20:34:34 UTC |
| 5a3810a | dmorton | 27 April 2015, 00:55:59 UTC | Genome::Process can run without using lsf slot Instead of bsub'ing a process that runs a workflow, this allows PTero to run a workflow that has been modified to include steps that update the status on the Genome::Process | 29 April 2015, 20:34:34 UTC |
| 58dd62b | dmorton | 27 April 2015, 00:50:49 UTC | Sanitize %ENV The value undef is not a valid Environment Variable value. This doesn't cause Perl any issues, but it does cause problems when we pass this to another process and they try to set the environment. | 29 April 2015, 20:34:34 UTC |
| 14f7985 | dmorton | 25 April 2015, 20:33:04 UTC | WorkflowBuilder can submit Genome::Process workflows without blocking The Genome::Process gets its status updated using 'genome process update-status' during the workflow. The original workflow gets wrapped in an outer workflow that sets the 'running', and 'failed', 'succeeded' status appropriately. This will make it possible to submit a workflow on behalf of a Genome::Process without consuming a workflow lsf queue slot. | 29 April 2015, 20:34:33 UTC |
| 68edcbb | dmorton | 25 April 2015, 20:25:54 UTC | Add ability to set exit code This command needs to sometimes exit 1 (fail) and sometimes exit 0 (succeed) regardless of it successfully doing its work. It will be used similarly to a 'shortcut' step in a workflow, and should always exit 1 when used in that way. It will also be used normally in a workflow, and should always exit 0 when used in that way. | 29 April 2015, 20:31:04 UTC |
| d8b0c67 | dmorton | 23 April 2015, 17:31:59 UTC | Add command to set the status of a Genome::Process | 29 April 2015, 20:31:03 UTC |
| a776cc6 | Nathaniel Nutter | 29 April 2015, 20:20:12 UTC | show stderr when trying to load module for assert_module_found If there is an error trying to use the module then this will show it. | 29 April 2015, 20:20:12 UTC |
| 6d37f98 | Thomas Mooney | 29 April 2015, 19:15:43 UTC | Whitespace. | 29 April 2015, 19:15:43 UTC |
| a52c8d8 | Thomas Mooney | 29 April 2015, 19:15:12 UTC | Remove code inside an if (0) since 2012. | 29 April 2015, 19:15:12 UTC |
| e150375 | Nathaniel Nutter | 29 April 2015, 18:49:36 UTC | Merge pull request #697 from nnutter/RT-105443 improve error message when trying to rename across devices | 29 April 2015, 18:49:36 UTC |
| 179f497 | Thomas Mooney | 29 April 2015, 18:08:43 UTC | Separately track the list of all the chromosomes we've seen. | 29 April 2015, 18:08:43 UTC |
| 94fca07 | Susanna Siebert | 29 April 2015, 17:38:25 UTC | Merge pull request #686 from susannasiebert/variant_reporting_vcf Write individual soft filter results to the vcf report | 29 April 2015, 17:38:25 UTC |
| 9e6299b | Thomas Mooney | 29 April 2015, 17:24:13 UTC | Only keep open up to 100 filehandles. | 29 April 2015, 17:24:13 UTC |
| c0da4f0 | Thomas Mooney | 29 April 2015, 17:11:50 UTC | Use Genome::Sys->create_temp_directory so LSF-provided dir is used. | 29 April 2015, 17:11:50 UTC |
| 575b9f7 | Allison Penner Regier | 29 April 2015, 16:03:14 UTC | Merge pull request #699 from apregier/vep_fix Need to pass users to nested results | 29 April 2015, 16:03:14 UTC |
| 53a3f96 | Thomas Mooney | 29 April 2015, 15:14:25 UTC | Bump memory request to 512 MB. | 29 April 2015, 15:14:25 UTC |
| fcccfda | Thomas Mooney | 29 April 2015, 14:06:53 UTC | Use the labelled merged result. The "refinements" each produce separate merged BAMs, so picking the first one we run across is not guaranteed to get the final BAM. | 29 April 2015, 14:06:53 UTC |
| 2d9a92c | Avinash Ramu | 28 April 2015, 22:49:07 UTC | Merge pull request #685 from gatoravi/igv_link IGV link | 28 April 2015, 22:49:07 UTC |
| d3e4e4a | apregier | 28 April 2015, 21:06:39 UTC | Need to pass users to nested results | 28 April 2015, 21:06:39 UTC |
| f904204 | Avinash Ramu | 28 April 2015, 20:32:34 UTC | blessed build with dgidb results | 28 April 2015, 20:32:34 UTC |
| 4a03fb5 | Nathaniel Nutter | 28 April 2015, 19:37:09 UTC | do not follow symlink when determining device of file | 28 April 2015, 19:37:09 UTC |
| 1512c38 | APipe Tester | 28 April 2015, 18:10:19 UTC | updated jenkins submodule to a314ce5 | 28 April 2015, 18:10:19 UTC |
| 57c89c1 | Nathaniel Nutter | 28 April 2015, 16:47:07 UTC | improve error message when trying to rename across devices | 28 April 2015, 18:02:07 UTC |
| e7a1b54 | Avinash Ramu | 28 April 2015, 17:43:57 UTC | Merge branch 'master' into igv_link | 28 April 2015, 17:43:57 UTC |
| 358d421 | Susanna Siebert | 28 April 2015, 13:09:48 UTC | Merge pull request #695 from susannasiebert/bam_size Get bam size from get_bam_file instead of from alignment_bam_file_paths | 28 April 2015, 13:09:48 UTC |
| eb67f13 | APipe Tester | 28 April 2015, 12:17:33 UTC | Updated `gmt` tab completion. | 28 April 2015, 12:17:33 UTC |
| 359fadc | APipe Tester | 28 April 2015, 12:16:43 UTC | Updated `genome` tab completion. | 28 April 2015, 12:16:43 UTC |
| 1a2d27c | APipe Tester | 28 April 2015, 12:14:57 UTC | Updated class browser cache. | 28 April 2015, 12:14:57 UTC |
| 75b1575 | Eddie Belter | 27 April 2015, 23:12:40 UTC | Merge pull request #657 from ebelter/cghub GMT CG Hub - Add command to help TCGA imports | 27 April 2015, 23:12:40 UTC |
| 6fe7125 | Eddie Belter | 27 April 2015, 22:02:39 UTC | GMT CG Hub: spell check | 27 April 2015, 22:02:39 UTC |
| 5dfcaa0 | Eddie Belter | 27 April 2015, 22:00:41 UTC | Cg Hub Metadata: use isa => __PACKAGE__ when validating params | 27 April 2015, 22:00:41 UTC |
| f262582 | Eddie Belter | 27 April 2015, 21:57:23 UTC | CG Hub: just return the result value | 27 April 2015, 21:57:23 UTC |
| 84a1afd | Susanna Siebert | 27 April 2015, 21:54:43 UTC | Ensure that we query the database and don't just get the cached value | 27 April 2015, 21:54:43 UTC |
| 1084252 | Susanna Siebert | 27 April 2015, 21:49:58 UTC | use correct variables | 27 April 2015, 21:49:58 UTC |
| 58dc2b8 | Susanna Siebert | 27 April 2015, 21:12:39 UTC | Better error message | 27 April 2015, 21:12:39 UTC |
| 15bd279 | Susanna Siebert | 27 April 2015, 21:12:19 UTC | check again if the bam_size has been set in the meantime since get_bam_file can take a long time | 27 April 2015, 21:12:19 UTC |
| 5d1a6f4 | Susanna Siebert | 27 April 2015, 20:34:12 UTC | Fix bugs in unless-statement | 27 April 2015, 20:34:12 UTC |
| 38234de | Susanna Siebert | 27 April 2015, 20:16:58 UTC | Move set_bam_size outside of if-clause | 27 April 2015, 20:16:58 UTC |
| dd025b9 | Susanna Siebert | 27 April 2015, 20:14:45 UTC | Add more checking around the bam file to ensure that it really exists | 27 April 2015, 20:14:45 UTC |
| a90d85a | Feiyu Du | 27 April 2015, 20:08:05 UTC | Merge pull request #692 from dufeiyu/bam_size Set bam_size regardless of _use_alignment_summary_cpp | 27 April 2015, 20:08:05 UTC |
| de54126 | Susanna Siebert | 27 April 2015, 18:53:53 UTC | use set_bam_size subroutine | 27 April 2015, 18:53:53 UTC |
| 0303cc5 | Susanna Siebert | 27 April 2015, 18:49:36 UTC | Use correct method get_bam_file | 27 April 2015, 18:49:36 UTC |
| d910612 | Susanna Siebert | 27 April 2015, 18:15:43 UTC | get bam size from get_bam_file instead of from alignment_bam_file_paths | 27 April 2015, 18:15:43 UTC |
| 1630762 | APipe Tester | 25 April 2015, 21:18:31 UTC | updated ur submodule to 1cd191b | 25 April 2015, 21:18:31 UTC |
| fdfd83c | David Morton | 25 April 2015, 19:53:19 UTC | Merge pull request #689 from davidlmorton/fix_encoding Encode/Decode workflow inputs and outputs when using PTero | 25 April 2015, 19:53:19 UTC |
| b763b2e | Nathaniel Nutter | 25 April 2015, 05:40:56 UTC | Merge pull request #693 from iferguson90/picard-simple-fix Stop picking up single jar versions of Picard. | 25 April 2015, 05:40:56 UTC |
| a679b33 | Ian Ferguson | 24 April 2015, 21:00:36 UTC | Stop picking up single jar versions of Picard. Prior to version 1.124, Picard was made up as a set of jars, one for each tool, installed under /usr/share/java/picard-toolsV.VVV/. Additionally, a support jar would be installed as /usr/share/java/picard-V.VVV.jar. Picard versions 1.124 and later use a single jar, installed as /usr/share/java/picard-V.VVV.jar, to provide all tools. The Picard GMT was picking up both single- and multi-jar versions of Picard, even though it could only handle the older multi-jar versions. This commit should prevent the Picard GMT from picking up the single-jar versions of Picard (1.124 and later) until single-jar support can be added. | 24 April 2015, 21:00:36 UTC |
| 7f3a9f3 | Nathaniel Nutter | 24 April 2015, 19:24:00 UTC | Merge pull request #691 from gatoravi/update_clinseq_blessed update clinseq blessed | 24 April 2015, 19:24:00 UTC |
| b5e3b29 | Avinash Ramu | 24 April 2015, 19:18:34 UTC | update clinseq blessed This is related to a new source - GuideToPharmacologyInteractions that was added to DGIdb. | 24 April 2015, 19:18:34 UTC |
| d8328ff | Nathaniel Nutter | 24 April 2015, 19:09:24 UTC | Merge pull request #690 from nnutter/clin-seq updated expected results for Genome/Model/ClinSeq/Command/AnnotateGenesByDgidb.t | 24 April 2015, 19:09:24 UTC |
| 2b3d831 | Feiyu Du | 24 April 2015, 18:51:15 UTC | set bam_size regardless of _use_alignment_summary_cpp | 24 April 2015, 18:51:15 UTC |
| 8b12655 | Nathaniel Nutter | 24 April 2015, 18:36:27 UTC | update expected results | 24 April 2015, 18:36:27 UTC |
| b4411a5 | Nathaniel Nutter | 24 April 2015, 18:35:47 UTC | fix warnings that occur when one file is longer than the other | 24 April 2015, 18:35:47 UTC |
| dfcb1ee | Feiyu Du | 24 April 2015, 17:12:54 UTC | Merge pull request #687 from dufeiyu/unlock Use Scope::Guard to ensure unlocking | 24 April 2015, 17:12:54 UTC |
| 9da822e | dmorton | 24 April 2015, 15:43:00 UTC | Encode/Decode workflow inputs and outputs We were already doing this for steps within a workflow, but some workflows take objects as inputs and return objects as outputs. This allows that to work. | 24 April 2015, 15:43:00 UTC |
| 103d122 | Avinash Ramu | 24 April 2015, 15:37:38 UTC | update clinseq blessed, igv_link | 24 April 2015, 15:37:38 UTC |
| ce6e85a | Avinash Ramu | 24 April 2015, 15:22:20 UTC | factor out the column names | 24 April 2015, 15:22:20 UTC |
| f1d2cba | APipe Tester | 24 April 2015, 12:24:59 UTC | Updated `gmt` tab completion. | 24 April 2015, 12:24:59 UTC |
| fd17962 | APipe Tester | 24 April 2015, 12:24:15 UTC | Updated `genome` tab completion. | 24 April 2015, 12:24:15 UTC |
| c6c4d05 | APipe Tester | 24 April 2015, 12:22:21 UTC | Updated class browser cache. | 24 April 2015, 12:22:21 UTC |
| 476be02 | Feiyu Du | 23 April 2015, 20:53:53 UTC | use Scope::Guard to make sure unlocking | 23 April 2015, 20:53:53 UTC |
| a7793d6 | Susanna Siebert | 23 April 2015, 18:12:16 UTC | Update blessed trio process test | 23 April 2015, 18:12:16 UTC |
| 97b0955 | Adam Coffman | 23 April 2015, 16:59:01 UTC | Merge pull request #683 from tmooney/delete_files_in_our_directory Delete the output files, not whatever is in the current directory. | 23 April 2015, 16:59:01 UTC |
| 17ea251 | Indraniel | 23 April 2015, 16:00:30 UTC | Merge pull request #679 from indraniel/vcf-evaluate-pt2 GMT Integration of VCF Evaluation (part 2) | 23 April 2015, 16:00:30 UTC |
| 2a405b3 | Gabriel Sanderson | 23 April 2015, 15:43:10 UTC | Merge pull request #681 from gsanders/bam_header_fix Create bam headers on demand | 23 April 2015, 15:43:10 UTC |
| 1a65280 | Susanna Siebert | 23 April 2015, 15:18:57 UTC | Write individual soft filter results to vcf | 23 April 2015, 15:18:57 UTC |
| d6ab3ec | Susanna Siebert | 23 April 2015, 13:22:52 UTC | remove intermediate subroutine | 23 April 2015, 15:18:31 UTC |
| 1a8b40a | Avinash Ramu | 23 April 2015, 15:16:06 UTC | add IGV link to SNVIndel report | 23 April 2015, 15:16:06 UTC |
| ad10282 | Avinash Ramu | 23 April 2015, 15:09:12 UTC | fix docs | 23 April 2015, 15:09:12 UTC |
| 66c5b32 | Gabriel Sanderson | 23 April 2015, 15:03:52 UTC | This unless is not necessary since create_bam_flagstat checks as well | 23 April 2015, 15:03:52 UTC |
| 19dea37 | David Morton | 22 April 2015, 22:35:17 UTC | Merge pull request #682 from davidlmorton/block_n_converge Support Converge Operations when using Ptero | 22 April 2015, 22:35:17 UTC |
| 871f7c8 | Gabriel Sanderson | 22 April 2015, 18:50:13 UTC | Refactor usage of create_bam_flagstat | 22 April 2015, 18:50:13 UTC |
| 9db8b02 | Thomas Mooney | 22 April 2015, 18:39:41 UTC | Delete the output files, not whatever is in the current dir! | 22 April 2015, 18:39:41 UTC |
| a008dba | Susanna Siebert | 22 April 2015, 17:31:54 UTC | Merge pull request #678 from susannasiebert/variant_reporting_vep Don't fail optional expert parameters as required during validation | 22 April 2015, 17:31:54 UTC |
| 7ea629a | Indraniel Das | 22 April 2015, 17:24:42 UTC | + apply @acoffman 's 3rd suggestion - use the TSV reader that's already in Genome::Utility | 22 April 2015, 17:24:42 UTC |
| 2dd0d15 | Indraniel Das | 22 April 2015, 17:01:32 UTC | + apply @tmooney 's 7th suggestion - ensure there's a space between the status message sentences when creating the output directory. | 22 April 2015, 17:01:32 UTC |
| 6c87f71 | Indraniel Das | 22 April 2015, 16:59:45 UTC | + apply @tmooney 's 6th suggestion - dynamically call the stat methods instead of explicitly. This makes the code shorter. | 22 April 2015, 16:59:45 UTC |
| ad6011c | dmorton | 22 April 2015, 15:46:46 UTC | Only get the first element of `output_properties` Legacy Converge operations would only supply outputs to the first specified output_property of the operation, even if multiple outputs were specified. | 22 April 2015, 15:46:46 UTC |
| e2337f7 | Susanna Siebert | 22 April 2015, 15:42:33 UTC | Move conversion to Set::Scalar into the subroutines | 22 April 2015, 15:42:33 UTC |
| cadb299 | Susanna Siebert | 21 April 2015, 19:45:50 UTC | Remove unused subroutine | 22 April 2015, 15:38:35 UTC |
| 6b0f861 | Avinash Ramu | 22 April 2015, 14:17:34 UTC | Merge pull request #680 from gatoravi/update_build_emailaddress use ENV variables to configure build email | 22 April 2015, 14:17:34 UTC |
| 8d1623e | APipe Tester | 22 April 2015, 12:16:34 UTC | Updated `genome` tab completion. | 22 April 2015, 12:16:34 UTC |
