| 4adcc98 | Thomas Mooney | 20 February 2013, 23:13:18 UTC | Call the method we think exists. | 20 February 2013, 23:13:18 UTC |
| 049fbc8 | Eddie Belter | 20 February 2013, 20:51:37 UTC | InstData: add tests for tgi_lims_status | 20 February 2013, 20:51:37 UTC |
| 0ce2950 | Eddie Belter | 20 February 2013, 20:49:04 UTC | InstData: added tgi_lims_status convenience method; need to rename to something not tgi specific | 20 February 2013, 20:49:04 UTC |
| da79817 | Eddie Belter | 20 February 2013, 20:13:21 UTC | Sync: solexa inst data was not adding tgi_lims_status | 20 February 2013, 20:13:21 UTC |
| 3436a0d | Feiyu Du | 20 February 2013, 19:54:41 UTC | replace the abandoned test build with a new succeeded one and update the test data accordingly | 20 February 2013, 19:54:41 UTC |
| db316f7 | Ian Ferguson | 20 February 2013, 19:37:54 UTC | Added iferguso to underallocated volume emails | 20 February 2013, 19:37:54 UTC |
| fa32cdf | Veena Bhonagiri | 20 February 2013, 18:58:02 UTC | Merge branch 'master' of git+ssh://git/srv/git/genome | 20 February 2013, 18:58:02 UTC |
| a49492e | Veena Bhonagiri | 20 February 2013, 18:54:11 UTC | Modified so the script can handle any number after DFT,MSI,FNL & TST for locus tag suffix | 20 February 2013, 18:54:11 UTC |
| caf33b9 | Travis Abbott | 20 February 2013, 08:36:41 UTC | add bwa 0.6.2 | 20 February 2013, 08:36:41 UTC |
| cc3a59a | Nathan Nutter | 19 February 2013, 23:54:02 UTC | localize the CHLD handler | 19 February 2013, 23:54:11 UTC |
| 29a0547 | Nathan Nutter | 16 February 2013, 00:45:43 UTC | add .mailmap | 19 February 2013, 23:54:10 UTC |
| 664a1b2 | Mark Burnett | 19 February 2013, 23:05:18 UTC | make sure logDir gets set in Workflox XML This change is related to the workflow replacement. ReferenceAlignment was not setting its logDir. | 19 February 2013, 23:16:49 UTC |
| 4d1e909 | APipe Tester | 19 February 2013, 22:18:04 UTC | Updated `genome` tab completion. | 19 February 2013, 22:18:04 UTC |
| ae85949 | APipe Tester | 19 February 2013, 21:36:51 UTC | Updated `gmt` tab completion. | 19 February 2013, 21:36:53 UTC |
| be5eefd | APipe Tester | 19 February 2013, 21:35:49 UTC | Updated `genome` tab completion. | 19 February 2013, 21:36:52 UTC |
| 41719c8 | apregier | 19 February 2013, 21:16:18 UTC | Merge branch 'updated2' into gb_master | 19 February 2013, 21:16:18 UTC |
| d7b9e82 | apregier | 19 February 2013, 20:57:48 UTC | Add dbvar importer | 19 February 2013, 21:15:56 UTC |
| b0ab3ee | Mark Burnett | 19 February 2013, 15:30:27 UTC | make SoftwareResult::get less noisy it will no longer spew error messages when called in array or void context | 19 February 2013, 21:09:46 UTC |
| c6e0e24 | APipe Tester | 19 February 2013, 20:47:08 UTC | Updated `genome` tab completion. | 19 February 2013, 20:48:05 UTC |
| 58d92df | Travis Abbott | 19 February 2013, 20:41:24 UTC | check errors in gmt tabix list-chromosomes | 19 February 2013, 20:41:24 UTC |
| c3c0c58 | Travis Abbott | 08 February 2013, 00:51:31 UTC | remove unused package var | 19 February 2013, 20:40:33 UTC |
| 83065d9 | Eddie Belter | 19 February 2013, 20:22:12 UTC | Phenotype Corr Casr Control Unrelated: ability to add lsf resource to operations; add 32 Mb mem for create single variant matrix | 19 February 2013, 20:22:47 UTC |
| 49508f2 | apregier | 19 February 2013, 19:43:55 UTC | Merge branch 'updated2' into gb_master | 19 February 2013, 19:43:55 UTC |
| 697fc06 | apregier | 19 February 2013, 19:42:18 UTC | Option to annotate genes within n bp of breakpoints | 19 February 2013, 19:43:28 UTC |
| 653058a | apregier | 19 February 2013, 19:39:38 UTC | Give the flanking size as a parameter | 19 February 2013, 19:43:27 UTC |
| f87fcf5 | Eddie Belter | 19 February 2013, 17:50:58 UTC | Phenotype Corr: do not pass undef vars through to tools. | 19 February 2013, 17:51:08 UTC |
| c4e9f14 | Ben Oberkfell | 19 February 2013, 17:23:48 UTC | widen metric name | 19 February 2013, 17:23:48 UTC |
| ea0b54f | apregier | 18 February 2013, 22:10:36 UTC | Merge branch 'updated2' into gb_master | 18 February 2013, 22:10:36 UTC |
| 848240a | apregier | 18 February 2013, 22:10:14 UTC | FusionTranscripts requires orientation | 18 February 2013, 22:10:24 UTC |
| 38e8fc5 | apregier | 18 February 2013, 21:38:01 UTC | Refactor | 18 February 2013, 22:10:23 UTC |
| d0b1455 | Gabriel Sanderson | 18 February 2013, 21:12:29 UTC | Merge branch 'master' into gb_master | 18 February 2013, 21:12:29 UTC |
| 0dfdd5b | Gabriel Sanderson | 18 February 2013, 21:12:03 UTC | Added a ValidateLargeIndels.pm to get to the underlying commands | 18 February 2013, 21:12:03 UTC |
| daeda69 | Thomas Mooney | 18 February 2013, 20:49:58 UTC | Change instrument data linkage to be more specific so UR doesn't complain. | 18 February 2013, 20:49:58 UTC |
| c38913f | apregier | 18 February 2013, 20:43:18 UTC | Merge branch 'updated2' into gb_master | 18 February 2013, 20:43:18 UTC |
| 867e44f | apregier | 18 February 2013, 20:36:57 UTC | Allow user to specify which columns are which in input format | 18 February 2013, 20:41:32 UTC |
| 0c67b41 | apregier | 18 February 2013, 17:16:43 UTC | First pass at repeatmasker annotation | 18 February 2013, 20:41:32 UTC |
| 64fdb35 | apregier | 18 February 2013, 17:16:09 UTC | RepeatMasker annotation importer | 18 February 2013, 20:41:31 UTC |
| 747618c | Thomas Mooney | 18 February 2013, 18:40:36 UTC | Now that the display name has fancy characters, be careful what we name files. | 18 February 2013, 18:40:36 UTC |
| a4b9516 | Thomas Mooney | 18 February 2013, 18:15:58 UTC | Use the currently-running intepreter rather than `perl`. | 18 February 2013, 18:15:58 UTC |
| 627f24a | Chris Miller | 18 February 2013, 18:03:07 UTC | updates to samtools options | 18 February 2013, 18:03:18 UTC |
| c7c0930 | Obi Griffith | 17 February 2013, 17:31:48 UTC | fixed path for cufflinks files | 17 February 2013, 17:31:48 UTC |
| c8ecc1e | Gabriel Sanderson | 16 February 2013, 00:58:57 UTC | Merge branch 'validation' into gb_master | 16 February 2013, 00:58:57 UTC |
| d4bad26 | Gabriel Sanderson | 14 February 2013, 21:22:13 UTC | Include both the indel validation list and the DV2 file if they exist. Skip detect variants if strategies are undef Skip IdentifyDnp if no snv_detection_strategy. Skip Review Variants if no snv detection strategy is set | 16 February 2013, 00:57:16 UTC |
| ef3cc88 | Mark Burnett | 15 February 2013, 18:33:18 UTC | make SoftwareResult->get noisy | 15 February 2013, 21:40:49 UTC |
| 3c17bdc | Mark Burnett | 15 February 2013, 18:32:02 UTC | change refalign SoftwareResult->get to get_with_lock this was an indirect call made by most (all?) refalign builds | 15 February 2013, 21:40:49 UTC |
| 7902b59 | Scott Smith | 15 February 2013, 19:50:15 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 15 February 2013, 19:50:15 UTC |
| f9e48de | Jason Walker | 15 February 2013, 19:21:56 UTC | Fix the default_value and set as one of the example_values. Also start using Bio::DB::Sam now that we are on perl5.10 or greater. | 15 February 2013, 19:21:56 UTC |
| 362a00f | Jason Walker | 15 February 2013, 19:16:30 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 15 February 2013, 19:16:30 UTC |
| 4370b62 | Jason Walker | 15 February 2013, 19:16:22 UTC | Convert commented default_value to one of the example_values. | 15 February 2013, 19:16:22 UTC |
| 2d3537f | dmorton | 15 February 2013, 18:25:47 UTC | Reorganize Chimerascan tests | 15 February 2013, 18:34:42 UTC |
| 63fbd6c | Malachi Griffith | 15 February 2013, 16:40:08 UTC | Blessing new clin-seq build for 5.10-clinseq-wer to allow for updates to mutation-spectrum-sequence-context analysis | 15 February 2013, 16:40:08 UTC |
| 291328b | Scott Smith | 15 February 2013, 16:31:19 UTC | updated to not let people delete things with the lister | 15 February 2013, 16:31:19 UTC |
| 503afcd | Scott Smith | 15 February 2013, 15:58:12 UTC | back-ported Tom's UR fix for listers to Genome so that people at the lister demo won't have to -I in a UR checkout (remove lateer/redundant) | 15 February 2013, 15:58:12 UTC |
| dc06906 | Charles Lu | 15 February 2013, 00:32:38 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 15 February 2013, 00:32:38 UTC |
| 0638961 | Charles Lu | 15 February 2013, 00:32:33 UTC | updated MutationSpectrumSequenceContext.pm to give better plots and performs proportion test | 15 February 2013, 00:32:33 UTC |
| 38751c0 | Obi Griffith | 14 February 2013, 23:19:35 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 14 February 2013, 23:19:35 UTC |
| 954e66e | Obi Griffith | 14 February 2013, 23:19:09 UTC | Fixed bug in ignore-models-matching option | 14 February 2013, 23:19:09 UTC |
| a9e25a8 | Nathan Dees | 14 February 2013, 23:02:07 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 14 February 2013, 23:02:07 UTC |
| 683bba5 | Nathan Dees | 14 February 2013, 23:01:47 UTC | adjusted parameter name in bam-readcount call | 14 February 2013, 23:01:47 UTC |
| e9cd3ac | dmorton | 14 February 2013, 22:47:19 UTC | Fix ChimerascanResult using position sorted bam aligned_reads.bam must be query_name sorted and we were symlinking in something that was position sorted like the sorted_aligned_reads.bam not thinking it was using the aligned_reads.bam for anything, but it is using it to determine the insert-size distribution and relying on it being query_name sorted. | 14 February 2013, 22:49:23 UTC |
| 0c53715 | dmorton | 14 February 2013, 20:57:34 UTC | Sys doesn't assume /tmp is temp_dir Uses File::Spec->tmpdir() instead | 14 February 2013, 21:58:58 UTC |
| eb2175b | Chris Miller | 14 February 2013, 21:50:13 UTC | Added submodule sciClone | 14 February 2013, 21:50:13 UTC |
| 69772f2 | Chris Miller | 14 February 2013, 21:47:21 UTC | removing cloneCaller | 14 February 2013, 21:47:21 UTC |
| e9c4b8f | Chris Miller | 14 February 2013, 21:35:10 UTC | removing cloneCaller (to be renamed to sciClone) | 14 February 2013, 21:44:39 UTC |
| 00d3406 | Thomas Mooney | 14 February 2013, 21:34:23 UTC | Quiet warnings when working with blank lines. | 14 February 2013, 21:34:23 UTC |
| 30d2c15 | apregier | 14 February 2013, 21:31:48 UTC | Merge branch 'updated2' into gb_master | 14 February 2013, 21:31:48 UTC |
| 54c171a | apregier | 14 February 2013, 21:31:11 UTC | Change - to N/A | 14 February 2013, 21:31:35 UTC |
| 1399860 | Nathan Dees | 14 February 2013, 21:06:29 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 14 February 2013, 21:06:29 UTC |
| d5f6a7e | Nathan Dees | 14 February 2013, 21:06:24 UTC | added back in Allison's code to use g m t sam readcount | 14 February 2013, 21:06:24 UTC |
| c589d13 | dmorton | 14 February 2013, 20:54:18 UTC | Make ChimerascanResult use qname sorted bam | 14 February 2013, 20:55:23 UTC |
| 5a6c38a | apregier | 14 February 2013, 20:49:20 UTC | Merge branch 'updated2' into gb_master | 14 February 2013, 20:49:20 UTC |
| 1bed7d2 | apregier | 14 February 2013, 20:17:57 UTC | Automatically gather params from sub-annotators | 14 February 2013, 20:48:45 UTC |
| 6f9ec5a | APipe Tester | 14 February 2013, 19:40:34 UTC | updated jenkins submodule to ff739be | 14 February 2013, 19:40:34 UTC |
| 9f58d8c | Brian Derickson | 14 February 2013, 19:22:41 UTC | added research to valid disk groups | 14 February 2013, 19:22:48 UTC |
| 28f7bf2 | Jason Walker | 14 February 2013, 18:26:01 UTC | Add queryname sort before the SamToFastq conversion to reduce memory requirement. | 14 February 2013, 18:26:01 UTC |
| c245d12 | Gabriel Sanderson | 14 February 2013, 18:17:36 UTC | Merge branch 'validation' into gb_master | 14 February 2013, 18:17:36 UTC |
| 002a34e | Gabriel Sanderson | 14 February 2013, 18:17:13 UTC | Added a few values that were missing in _resolve_inputs when given a build and not other properties. | 14 February 2013, 18:17:13 UTC |
| a3c2dc6 | Nathan Nutter | 14 February 2013, 17:53:32 UTC | should not assume merged_alignment_bam_path exists | 14 February 2013, 17:53:32 UTC |
| 5d0a417 | Nathan Nutter | 14 February 2013, 17:03:17 UTC | allow Rest.psgi to have CPU and memory usage limited Our web workers fairly frequently persist for many minutes and/or use a lot of memory so we should be able to limit their CPU and memory usage. | 14 February 2013, 17:03:17 UTC |
| 68ff363 | Nathan Nutter | 14 February 2013, 17:00:22 UTC | update clinseq-wer blessed build | 14 February 2013, 17:00:22 UTC |
| 378ae8e | Thomas Mooney | 14 February 2013, 15:34:10 UTC | Set a memory request. A recent run took 11.5GB, so set this to 14GB for now. | 14 February 2013, 15:34:10 UTC |
| 8dcd449 | Thomas Mooney | 14 February 2013, 15:23:47 UTC | Updated blessedness after CNV fixes of RT#89648 | 14 February 2013, 15:23:47 UTC |
| 480f969 | dmorton | 14 February 2013, 00:15:05 UTC | Keep non-primary alignments when filtering with reuse_bam=1 option we now keep all alignments found in the Tophat BAM from the rna_seq pipeline. This resolves APIPE-2691. | 14 February 2013, 00:18:44 UTC |
| 321ac41 | dmorton | 13 February 2013, 16:20:58 UTC | ChimerascanResult adds transcripts to bam header This resolves APIPE-2690 | 14 February 2013, 00:18:44 UTC |
| 4276c4a | Nathan Nutter | 13 February 2013, 20:16:54 UTC | update log reader for new format | 13 February 2013, 22:54:55 UTC |
| bc41e80 | Nathan Nutter | 13 February 2013, 20:17:16 UTC | improve log format for better parsing | 13 February 2013, 22:54:54 UTC |
| d9a1686 | Nathan Nutter | 13 February 2013, 20:16:20 UTC | remove disk usage from build's web view | 13 February 2013, 22:54:54 UTC |
| 51adc2b | Scott Smith | 13 February 2013, 21:00:29 UTC | clinseq update-analysis suports --ignore-models-matching=EXPR, and shows full display names on somatic models | 13 February 2013, 21:00:29 UTC |
| 1f05d9e | APipe Tester | 13 February 2013, 20:46:19 UTC | Updated `gmt` tab completion. | 13 February 2013, 20:46:19 UTC |
| 0718dc4 | APipe Tester | 13 February 2013, 20:45:27 UTC | Updated `genome` tab completion. | 13 February 2013, 20:45:27 UTC |
| 8f28f60 | Nathan Dees | 13 February 2013, 18:53:52 UTC | added an option to use varscan readcount methods | 13 February 2013, 18:54:12 UTC |
| 43d90a7 | Feiyu Du | 13 February 2013, 16:33:52 UTC | Modify more to make FusionTranscripts fit Conflicts: lib/perl/Genome/Model/Tools/Annotate/Sv.pm lib/perl/Genome/Model/Tools/Annotate/Sv.t lib/perl/Genome/Model/Tools/Annotate/Sv/Base.pm | 13 February 2013, 18:25:00 UTC |
| 88d8d55 | apregier | 13 February 2013, 16:02:58 UTC | Merge branch 'updated2' into gb_master | 13 February 2013, 16:02:58 UTC |
| ad52019 | apregier | 13 February 2013, 16:01:45 UTC | Add dbsnp to annotate sv | 13 February 2013, 16:01:55 UTC |
| f127171 | Mark Burnett | 12 February 2013, 20:55:35 UTC | SoftwareResult::get_with_lock now "reloads" between gets AlignmentResult::Bwa no longer calls load | 12 February 2013, 20:56:43 UTC |
| 862d16b | Thomas Mooney | 12 February 2013, 19:43:01 UTC | Fix for relying on a genome build. | 12 February 2013, 19:43:01 UTC |
| dff72df | Nathan Dees | 12 February 2013, 16:43:44 UTC | for a commit Merge branch 'master' of ssh://git/srv/git/genome | 12 February 2013, 16:43:44 UTC |
| 8a03b85 | Nathan Dees | 12 February 2013, 16:32:16 UTC | commented FindBin use statements | 12 February 2013, 16:32:16 UTC |
| 4887867 | Jason Walker | 12 February 2013, 16:07:10 UTC | Lower RAM to 16G for Picard SamToFastq | 12 February 2013, 16:07:10 UTC |
| e33c7ca | Thomas Mooney | 12 February 2013, 15:38:28 UTC | Pass along the inputs we've declared. | 12 February 2013, 15:38:28 UTC |
