| 80f3a61 | APipe Tester | 30 November 2015, 21:46:49 UTC | updated ur submodule to 0346c3e | 30 November 2015, 21:46:49 UTC |
| 97cd34f | Susanna Kiwala | 30 November 2015, 15:02:16 UTC | Merge pull request #1079 from susannasiebert/epitope_prediction_parser Refactor of epitope prediction NetMHC parser | 30 November 2015, 15:02:16 UTC |
| 12d953f | APipe Tester | 26 November 2015, 13:16:26 UTC | Updated `genome` tab completion. | 26 November 2015, 13:16:26 UTC |
| 0536797 | Feiyu Du | 25 November 2015, 21:08:12 UTC | Merge pull request #1134 from dufeiyu/lsf_resource_dv2_dispatcher Increase memory limit of lsf_resource_dv2_dispatcher | 25 November 2015, 21:08:12 UTC |
| 137ee74 | Feiyu Du | 25 November 2015, 20:38:55 UTC | increase mem limit to prevent more build failures | 25 November 2015, 20:38:55 UTC |
| 8db4e56 | Thomas B. Mooney | 25 November 2015, 19:06:09 UTC | Merge pull request #1132 from tmooney/bsub_and_wait_completion Add missing word "for" in method name. | 25 November 2015, 19:06:09 UTC |
| a469278 | Thomas Mooney | 25 November 2015, 18:21:13 UTC | Add missing word "for" in method name. | 25 November 2015, 18:21:13 UTC |
| 11e9b33 | Susanna Kiwala | 25 November 2015, 18:09:58 UTC | Merge pull request #1130 from susannasiebert/qc_framework_verify_bam_id_vcf Make QC genotype VCF file an input to the SSG pipeline and use in verifyBamId | 25 November 2015, 18:09:58 UTC |
| b0de8e9 | mkiwala | 25 November 2015, 15:53:25 UTC | Merge pull request #1129 from mkiwala/ptero-lsf-parameters Set queue and projectName when getting ptero lsf params | 25 November 2015, 15:53:25 UTC |
| ef99a04 | APipe Tester | 25 November 2015, 13:16:39 UTC | Updated `genome` tab completion. | 25 November 2015, 13:16:39 UTC |
| 1dc02d8 | APipe Tester | 25 November 2015, 13:15:05 UTC | Updated class browser cache. | 25 November 2015, 13:15:05 UTC |
| e0bef5e | Thomas B. Mooney | 24 November 2015, 22:26:57 UTC | Merge pull request #1091 from tmooney/unarchive_requires_analysis_project Unarchiving now requires an AnP instead of a lab. | 24 November 2015, 22:26:57 UTC |
| 7818afb | Thomas B. Mooney | 24 November 2015, 20:58:01 UTC | Merge pull request #1126 from tmooney/haplotype_caller_reserves_lsf_resource Set a default resource request for the BucketIterator. | 24 November 2015, 20:58:01 UTC |
| 7e274c2 | Susanna Kiwala | 24 November 2015, 20:57:54 UTC | Inputs should be obtained from the build, not the model | 24 November 2015, 20:57:54 UTC |
| bb2bb49 | Michael J. Kiwala | 24 November 2015, 20:46:33 UTC | Options in the lsf resource string take precedence | 24 November 2015, 20:46:33 UTC |
| eec8d47 | David Morton | 24 November 2015, 18:56:51 UTC | Merge pull request #1108 from davidlmorton/ptero_integration_tests_command Convert Ptero/IntegrationTest.pl into a Command | 24 November 2015, 18:56:51 UTC |
| d1b7b1e | Michael J. Kiwala | 24 November 2015, 17:09:04 UTC | Set queue and projectName when getting ptero lsf params | 24 November 2015, 17:09:04 UTC |
| da5e483 | Susanna Kiwala | 24 November 2015, 16:20:42 UTC | Update docs | 24 November 2015, 16:48:22 UTC |
| e29383c | Susanna Kiwala | 24 November 2015, 16:07:09 UTC | Test new genotype_vcf_file subroutine for VerifyBamId | 24 November 2015, 16:48:22 UTC |
| bdb53f2 | Susanna Kiwala | 24 November 2015, 16:06:32 UTC | New subroutine on VerifyBamID QC tool to use qc_genotype_vcf_file | 24 November 2015, 16:48:22 UTC |
| be10d97 | Susanna Kiwala | 24 November 2015, 16:05:54 UTC | Test qc_genotype_vcf_file handling in the SSG QC step | 24 November 2015, 16:48:22 UTC |
| 7fe7f44 | Susanna Kiwala | 24 November 2015, 16:05:01 UTC | Make qc_genotype_vcf_file an input to the SSG pipeline and pass along to the QC step | 24 November 2015, 16:48:22 UTC |
| 2d898e1 | Susanna Kiwala | 24 November 2015, 16:47:59 UTC | Merge pull request #1120 from susannasiebert/qc_framework_verify_bam_id_vcf New classes to store custom files as a software result | 24 November 2015, 16:47:59 UTC |
| 8df40f9 | Susanna Kiwala | 24 November 2015, 16:37:08 UTC | Use Carp::confess instead of $self->fatal_message | 24 November 2015, 16:37:08 UTC |
| f9f9f48 | David Morton | 24 November 2015, 01:22:10 UTC | Use Genome->base_dir | 24 November 2015, 01:22:10 UTC |
| 8bad304 | Feiyu Du | 23 November 2015, 22:15:03 UTC | Merge pull request #1128 from dufeiyu/tcga Add more TCGA name mapping | 23 November 2015, 22:15:03 UTC |
| 09a0c8d | Feiyu Du | 23 November 2015, 21:09:38 UTC | Add more name mapping | 23 November 2015, 21:09:38 UTC |
| d8aae02 | Anthony Brummett | 23 November 2015, 20:41:52 UTC | Merge pull request #1124 from brummett/notify-apipe-tester-apipe-queue Notify me when apipe-builder uses the apipe queue | 23 November 2015, 20:41:52 UTC |
| 8ba03c4 | David Morton | 23 November 2015, 20:20:28 UTC | Merge pull request #1127 from davidlmorton/process_view_notes Don't try to format body_text when displaying notes. | 23 November 2015, 20:20:28 UTC |
| fc8f689 | Anthony Brummett | 23 November 2015, 17:42:16 UTC | get more info out of LSF before emailing | 23 November 2015, 19:44:47 UTC |
| 123f6f7 | dmorton | 20 November 2015, 19:46:45 UTC | Don't try to format body_text when displaying notes. The clean_up_timestamp was throwing away everything after the first '.' which isn't desired here. | 20 November 2015, 19:46:45 UTC |
| 8c19512 | Susanna Kiwala | 20 November 2015, 16:12:02 UTC | whitespace fix | 20 November 2015, 16:12:02 UTC |
| 5b9501a | Susanna Kiwala | 20 November 2015, 16:11:38 UTC | Output the software result ID during post_get_or_create | 20 November 2015, 16:11:38 UTC |
| 59c8494 | Susanna Kiwala | 20 November 2015, 16:11:14 UTC | Add a doc line to the import command | 20 November 2015, 16:11:14 UTC |
| a9a1595 | Feiyu Du | 19 November 2015, 23:03:36 UTC | Merge pull request #1117 from dufeiyu/tcga Several improvements for TCGA submission | 19 November 2015, 23:03:36 UTC |
| c72b2ca | Feiyu Du | 19 November 2015, 22:00:54 UTC | remove unnecessary check | 19 November 2015, 22:00:54 UTC |
| 8d08051 | Susanna Kiwala | 19 November 2015, 21:36:51 UTC | New command to import genotype VCF file for QC | 19 November 2015, 21:36:51 UTC |
| 716fdb7 | Susanna Kiwala | 19 November 2015, 21:35:37 UTC | Need to modify the lookup_hash in ImportedFile in order for it to work with DelegatesToResult command | 19 November 2015, 21:36:03 UTC |
| 3d19c10 | Susanna Kiwala | 19 November 2015, 21:33:53 UTC | StageableSimple::SingleFile should be abstract | 19 November 2015, 21:33:53 UTC |
| 09855e3 | Susanna Kiwala | 19 November 2015, 21:33:31 UTC | abs_path the source_file_path before symlinking | 19 November 2015, 21:33:31 UTC |
| e25d19c | Thomas Mooney | 19 November 2015, 21:31:28 UTC | Set a default resource request for the BucketIterator. | 19 November 2015, 21:31:28 UTC |
| b84478a | David Morton | 19 November 2015, 18:12:55 UTC | Merge pull request #1123 from davidlmorton/remove_unused_input Remove clean_bam from workflow inputs | 19 November 2015, 18:12:55 UTC |
| f04749e | Anthony Brummett | 19 November 2015, 16:57:30 UTC | Send me an email when apipe-builder tries to use the apipe queue | 19 November 2015, 16:57:30 UTC |
| d1dc4b3 | Thomas B. Mooney | 18 November 2015, 22:37:07 UTC | Merge pull request #1121 from tmooney/hc_bucket_iterator_specifies_lsf_queue Specify an LSF queue for the bucket iterator. | 18 November 2015, 22:37:07 UTC |
| 5da3de4 | dmorton | 18 November 2015, 22:21:07 UTC | Remove clean_bam from workflow inputs It is not used in the workflow and WorkflowBuilder, when launching a PTero workflow disallows unused inputs. | 18 November 2015, 22:21:07 UTC |
| 7045cad | Susanna Kiwala | 18 November 2015, 21:45:03 UTC | Make a symlink in the staging directory instead of copying the file | 18 November 2015, 21:45:03 UTC |
| 15c2074 | Susanna Kiwala | 18 November 2015, 21:00:19 UTC | Fix subroutine name | 18 November 2015, 21:00:19 UTC |
| 233acab | Susanna Kiwala | 18 November 2015, 21:00:01 UTC | Implement _needs_symlinks_followed_when_syncing | 18 November 2015, 21:00:01 UTC |
| ece4601 | Anthony Brummett | 18 November 2015, 20:59:37 UTC | fix typo | 18 November 2015, 20:59:37 UTC |
| 9491295 | Susanna Kiwala | 18 November 2015, 20:59:36 UTC | Make source_file_path a metric and add the md5sum as an input | 18 November 2015, 20:59:36 UTC |
| b5a6005 | Anthony Brummett | 18 November 2015, 20:23:19 UTC | Make _valid_lsf_queue() more strict Use a normal string match instead of regex. Under the old code, "l" would have successfully matched against "long", even though "l" is not a valid queue name. | 18 November 2015, 20:23:19 UTC |
| e8e2a46 | Thomas Mooney | 18 November 2015, 20:10:22 UTC | Specify an LSF queue for the bucket iterator. | 18 November 2015, 20:11:07 UTC |
| a262c41 | Susanna Kiwala | 18 November 2015, 16:34:17 UTC | Make G::ID::Microarray::Result::Vcf inherit from StageableSimple::SingleFile | 18 November 2015, 17:38:20 UTC |
| f16de8b | Susanna Kiwala | 18 November 2015, 16:31:25 UTC | New class that uses StageableSimple::SingleFile to import a single file from a given path to an allocation | 18 November 2015, 17:38:20 UTC |
| 45468ac | Susanna Kiwala | 18 November 2015, 16:30:39 UTC | New StageableSimple subclass for a single file | 18 November 2015, 17:08:20 UTC |
| 35eb46a | mkiwala | 18 November 2015, 15:38:44 UTC | Merge pull request #1118 from mkiwala/ptero-submit-after-process-committed Ptero submit after process committed | 18 November 2015, 15:38:44 UTC |
| c7f8e23 | Thomas B. Mooney | 17 November 2015, 23:15:11 UTC | Merge pull request #1119 from tmooney/gatk_34_handles_gvcf_gz Add extra parameters when gzipped GVCF requested in version 3.4 of HaplotypeCaller. | 17 November 2015, 23:15:11 UTC |
| 7582f15 | Thomas Mooney | 17 November 2015, 21:56:44 UTC | Add in deprecated parameters when g.vcf.gz requested in 3.4. | 17 November 2015, 21:56:44 UTC |
| be47da4 | Feiyu Du | 17 November 2015, 21:52:53 UTC | check | 17 November 2015, 21:52:53 UTC |
| 20b9dba | Michael J. Kiwala | 17 November 2015, 17:08:25 UTC | Wait to submit to PTero until after the Genome::Process has been committed | 17 November 2015, 17:19:29 UTC |
| 95c960a | Michael J. Kiwala | 17 November 2015, 17:03:47 UTC | Use update_with_commit parameter to avoid committing too early Calling Genome::Process::Command::Run->create() without update_with_commit set to False, will cause a commit to happen before create() returns. In the case of the _submit_process function, which is used to submit a process's workflow to PTero, committing during Genome::Process::Command::Run->create() triggered an exception. Other functions in Genome::Process which also call Genome::Process::Command::Run->create() probably should set update_with_commit to False as well, but they are not currently having problems the way the are written. Those other calls should be investigated separately. | 17 November 2015, 17:19:29 UTC |
| da9a77d | APipe Tester | 17 November 2015, 13:16:45 UTC | Updated `genome` tab completion. | 17 November 2015, 13:16:45 UTC |
| 4398589 | APipe Tester | 17 November 2015, 13:15:12 UTC | Updated class browser cache. | 17 November 2015, 13:15:12 UTC |
| c6a6e6e | Feiyu Du | 16 November 2015, 20:23:20 UTC | add alternative way to decide whether sample is tumor or not from sample type code of tcga id | 16 November 2015, 20:23:20 UTC |
| fcb301a | Jim Eldred | 16 November 2015, 20:11:14 UTC | Merge pull request #1116 from tmooney/set_all_outputs_when_skipping_VLI_CACR Set all outputs regardless of why we're skipping. | 16 November 2015, 20:11:14 UTC |
| 769e8a0 | Thomas Mooney | 16 November 2015, 19:48:32 UTC | Set all outputs regardless of why we're skipping. | 16 November 2015, 19:48:32 UTC |
| 71a0886 | Jason Walker | 16 November 2015, 17:08:02 UTC | Merge pull request #1090 from jasonwalker80/copy_allocation Export/Copy Allocations to 'ad hoc' disk | 16 November 2015, 17:08:02 UTC |
| a56aa30 | Thomas B. Mooney | 16 November 2015, 16:36:46 UTC | Merge pull request #1102 from tmooney/send_alignment_dispatcher_to_long Use primary queue to submit SomVal AlignReads job. | 16 November 2015, 16:36:46 UTC |
| 3273a3e | Thomas B. Mooney | 16 November 2015, 16:35:29 UTC | Merge pull request #1104 from tmooney/shortcut_final_somval_steps Shortcut Several Skipped SomVal Steps | 16 November 2015, 16:35:29 UTC |
| d2a8cf6 | Jim Eldred | 16 November 2015, 16:32:52 UTC | Merge pull request #1115 from tmooney/haplotype_caller_vcf_naming Updates to HaplotypeCaller file naming in SSG | 16 November 2015, 16:32:52 UTC |
| 9791777 | Thomas Mooney | 16 November 2015, 16:07:26 UTC | Add tests that VCF is created as expected. | 16 November 2015, 16:07:26 UTC |
| c5ea958 | Thomas Mooney | 16 November 2015, 16:00:40 UTC | Use ".gz" extension so GATK produces a compressed VCF. | 16 November 2015, 16:00:40 UTC |
| bc0ec4f | Thomas Mooney | 16 November 2015, 15:59:55 UTC | Add an accessor for the VCF file. This way a lister can be used to obtain all the VCF results for a build with haplotype_caller_result.vcf_file | 16 November 2015, 15:59:55 UTC |
| 82dbf77 | Thomas Mooney | 16 November 2015, 15:59:12 UTC | Name the VCF result for the interval if there's only one. | 16 November 2015, 15:59:44 UTC |
| ea58c81 | David Morton | 14 November 2015, 03:48:23 UTC | Merge pull request #1113 from davidlmorton/dont_fail_ptero_builds Dont fail ptero builds | 14 November 2015, 03:48:23 UTC |
| af2f6b4 | Feiyu Du | 13 November 2015, 23:07:49 UTC | exclude the samples whose tcga_names are available via extraction_label or external_name | 13 November 2015, 23:07:49 UTC |
| 0bf3087 | Feiyu Du | 13 November 2015, 22:50:23 UTC | test new methods in unit test | 13 November 2015, 22:50:23 UTC |
| cd5d7e0 | dmorton | 13 November 2015, 22:16:28 UTC | Fix 'build scan' to ignore PTero run builds | 13 November 2015, 22:16:28 UTC |
| 7f4e6ad | dmorton | 13 November 2015, 22:15:08 UTC | Make and use Genome::Ptero::Utils This centeralizes url construction among other things. | 13 November 2015, 22:15:08 UTC |
| b2f7a87 | dmorton | 13 November 2015, 22:09:29 UTC | All reverse_as properties must be is_many even if in practice this will always return a single entity | 13 November 2015, 22:09:29 UTC |
| 123f9fa | Feiyu Du | 13 November 2015, 17:55:17 UTC | add more potential tcga naming candidates | 13 November 2015, 17:55:17 UTC |
| 6b4d878 | Feiyu Du | 13 November 2015, 17:29:30 UTC | Add alternative way to find sample tcga names | 13 November 2015, 17:29:30 UTC |
| ae7f129 | mkiwala | 13 November 2015, 01:45:33 UTC | Merge pull request #1111 from mkiwala/ptero-lsf-resources Get the lsf resource from the dag if they exist | 13 November 2015, 01:45:33 UTC |
| e98a302 | Feiyu Du | 12 November 2015, 23:00:07 UTC | bug fix | 12 November 2015, 23:00:07 UTC |
| c762a83 | Feiyu Du | 12 November 2015, 22:48:12 UTC | sort and align the list | 12 November 2015, 22:48:12 UTC |
| f5f263f | Susanna Kiwala | 12 November 2015, 22:18:05 UTC | Fix test data | 12 November 2015, 22:18:05 UTC |
| 46f6c33 | Feiyu Du | 12 November 2015, 22:15:56 UTC | Add TCGASpecialSampleNamingConversion.pm to hold special sample naming conversion | 12 November 2015, 22:15:56 UTC |
| 286538f | Thomas B. Mooney | 12 November 2015, 22:13:18 UTC | Merge pull request #1107 from tmooney/add_adders_to_ssg Add adders to SingleSampleGenotype Model. | 12 November 2015, 22:13:18 UTC |
| e62f2c6 | Michael J. Kiwala | 12 November 2015, 22:08:23 UTC | Get the lsf resource from the dag if they exist | 12 November 2015, 22:09:10 UTC |
| 1fa5e5e | Feiyu Du | 12 November 2015, 21:21:49 UTC | add alternative way to get tcga patient id | 12 November 2015, 21:21:49 UTC |
| 35e3540 | Thomas B. Mooney | 12 November 2015, 20:00:03 UTC | Merge pull request #1110 from tmooney/ssg_haplotype_caller_gets_correct_intervals Fix list evaluation in scalar context. | 12 November 2015, 20:00:03 UTC |
| df3dc46 | Thomas B. Mooney | 12 November 2015, 19:59:51 UTC | Merge pull request #1109 from tmooney/ssg_qc_requests_resource Add LSF queue and resource request to the SSG QC command. | 12 November 2015, 19:59:51 UTC |
| f86ce81 | Susanna Kiwala | 12 November 2015, 19:30:12 UTC | Merge pull request #1106 from susannasiebert/epitope_prediction_shortcut_fix Epitope prediction bugfixes | 12 November 2015, 19:30:12 UTC |
| bb49642 | Susanna Kiwala | 12 November 2015, 19:20:55 UTC | Add best match test for frameshifts | 12 November 2015, 19:29:17 UTC |
| 2ece9f3 | Susanna Kiwala | 12 November 2015, 16:41:24 UTC | Rework parsing algorithm Instead of matching MT and WT sub-peptide sequences based on the position we now pick the best match for a MT sub-peptide by finding the WT sub-peptide(s) with the highest number of matching AAs | 12 November 2015, 19:28:43 UTC |
| fabe2d5 | Susanna Kiwala | 11 November 2015, 16:04:56 UTC | Write longer frameshift WT subsequences necessary for downstream parsing | 12 November 2015, 19:28:43 UTC |
| f6af33c | Susanna Kiwala | 10 November 2015, 22:25:49 UTC | New subroutine that calculates the best WT sequence matches for a MT sequence | 12 November 2015, 19:28:40 UTC |
| 65b071e | mkiwala | 12 November 2015, 17:17:49 UTC | Merge pull request #1105 from mkiwala/alignment-dispatcher-logs Set logs recursively in alignment dispatcher | 12 November 2015, 17:17:49 UTC |
| d242b28 | Thomas Mooney | 12 November 2015, 15:46:10 UTC | Fix list evaluation in scalar context. | 12 November 2015, 15:46:10 UTC |
| 7bbdae5 | Thomas Mooney | 12 November 2015, 15:30:18 UTC | Add LSF queue and resource request to the SSG QC command. | 12 November 2015, 15:30:18 UTC |
