| 7640656 | apregier | 28 September 2012, 18:07:06 UTC | Add max_mem_gb param option for allpaths | 03 October 2012, 21:56:34 UTC |
| 0610077 | Anthony Brummett | 03 October 2012, 21:52:43 UTC | When determining a sire configuration module from a hostname, convert - to _ so it will be a valid Perl module name | 03 October 2012, 21:52:43 UTC |
| 78c758e | nnutter | 03 October 2012, 21:04:15 UTC | assign (un)archive to a job group | 03 October 2012, 21:07:01 UTC |
| dd0e5cb | Thomas Mooney | 03 October 2012, 20:20:40 UTC | Go back to using $model->real_input_properties so input names are displayed. | 03 October 2012, 20:20:40 UTC |
| 1eda1c4 | Thomas Mooney | 03 October 2012, 20:12:30 UTC | Use the $self-> calling convention for subroutines. | 03 October 2012, 20:12:30 UTC |
| 4961c22 | Thomas Mooney | 03 October 2012, 20:07:58 UTC | Use empty spacer when right-justifying names. Otherwise names one less than the desired length would end up left rather than right aligned. | 03 October 2012, 20:07:58 UTC |
| f02d364 | nnutter | 03 October 2012, 17:21:57 UTC | fix typo | 03 October 2012, 17:22:20 UTC |
| 0208d9d | Malachi Griffith | 03 October 2012, 16:49:00 UTC | Fix read counting bug in clinseq summarize-svs | 03 October 2012, 16:49:00 UTC |
| 1b3a0c4 | Charles Lu | 03 October 2012, 16:41:43 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 03 October 2012, 16:41:43 UTC |
| 2f79e8f | Charles Lu | 03 October 2012, 16:41:40 UTC | new R function to do pooled-burden test | 03 October 2012, 16:41:40 UTC |
| b533f93 | Nathan Nutter | 03 October 2012, 16:32:53 UTC | change a couple of copy-pasted blocks to use cached reference | 03 October 2012, 16:33:48 UTC |
| 5f58fd3 | Nathan Nutter | 03 October 2012, 16:24:13 UTC | get mm9 reference object and used cached path | 03 October 2012, 16:33:47 UTC |
| 4f4c990 | Nathan Nutter | 03 October 2012, 16:23:34 UTC | change a bunch of copy-pasted blocks to use cached reference | 03 October 2012, 16:33:25 UTC |
| f625a97 | Charles Lu | 03 October 2012, 15:51:43 UTC | added =cut POD directive to properly end POD section. | 03 October 2012, 15:51:43 UTC |
| 08206ff | APipe Tester | 03 October 2012, 14:07:16 UTC | updated workflow submodule to 6380275 | 03 October 2012, 14:07:16 UTC |
| c844517 | APipe Tester | 03 October 2012, 13:43:25 UTC | updated jenkins submodule to 1cba942 | 03 October 2012, 13:43:25 UTC |
| 5a23c98 | Travis Abbott | 02 October 2012, 23:11:54 UTC | add is_sample_filtered to Vcf::Entry | 02 October 2012, 23:12:09 UTC |
| 686ca0c | APipe Tester | 02 October 2012, 21:56:49 UTC | updated workflow submodule to c9c7838 | 02 October 2012, 21:56:49 UTC |
| e2fad5c | Travis Abbott | 02 October 2012, 21:40:26 UTC | make sure gene list in burden test summary has no dups | 02 October 2012, 21:43:03 UTC |
| 5ebd81f | Travis Abbott | 02 October 2012, 18:19:34 UTC | include all gene annotation in plots | 02 October 2012, 21:43:03 UTC |
| 66d50ad | Travis Abbott | 02 October 2012, 18:19:04 UTC | add peek to Vep::Reader | 02 October 2012, 21:43:03 UTC |
| c251f74 | Travis Abbott | 02 October 2012, 18:18:40 UTC | don't use UR for Vcf Entries | 02 October 2012, 21:43:02 UTC |
| 259f15f | Adam Coffman | 02 October 2012, 20:49:00 UTC | add picard 1.77 as an available version | 02 October 2012, 20:49:00 UTC |
| 6f3ca38 | Adam Coffman | 02 October 2012, 20:35:32 UTC | fall back on all_sequences.fa if all_sequences.bowtie is not present | 02 October 2012, 20:35:32 UTC |
| ea19296 | Adam Coffman | 02 October 2012, 20:28:30 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 02 October 2012, 20:28:30 UTC |
| 5a76fba | Adam Coffman | 02 October 2012, 20:27:11 UTC | Change gmt convert bed-to-annotation to use up to date algorithm Command will now take an input specifying which version of the annotator to use | 02 October 2012, 20:27:11 UTC |
| 72ec59c | Kyung Kim | 02 October 2012, 20:26:44 UTC | update output and create summary file | 02 October 2012, 20:26:44 UTC |
| 05a68ed | Thomas Mooney | 02 October 2012, 18:50:26 UTC | Provide for skipping NovoRealign if there were no SVs from Breakdancer. | 02 October 2012, 18:50:26 UTC |
| 32d5e02 | Nathan Dees | 02 October 2012, 15:42:21 UTC | removed default build 36 ref. added "SV_Contigs" to model names. | 02 October 2012, 15:42:21 UTC |
| 93b5112 | Nathan Dees | 02 October 2012, 15:40:09 UTC | fixed a scoping issue | 02 October 2012, 15:40:09 UTC |
| f0b02ea | Nathan Dees | 02 October 2012, 15:20:45 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 02 October 2012, 15:20:45 UTC |
| 53508b6 | Nathan Dees | 02 October 2012, 15:20:36 UTC | complete revamp | 02 October 2012, 15:20:36 UTC |
| 5344b76 | Thomas Mooney | 02 October 2012, 14:06:22 UTC | Tolerate no content_type when synchronizing FeatureLists from LIMS. | 02 October 2012, 14:06:22 UTC |
| 9e541bf | Malachi Griffith | 01 October 2012, 22:05:40 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 01 October 2012, 22:05:40 UTC |
| 641810a | Malachi Griffith | 01 October 2012, 22:05:32 UTC | Limit clinseq summarize builds to samples used in clinseq analysis instead of all samples associated with the patient | 01 October 2012, 22:05:32 UTC |
| f0626cb | Travis Abbott | 01 October 2012, 21:43:26 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 01 October 2012, 21:43:26 UTC |
| c4828af | Travis Abbott | 01 October 2012, 21:42:44 UTC | fix edge case in phenocorr clinical data parsing when a line ends with a delimiter, split won't give you an undef as the last field unless you specify a negative limit | 01 October 2012, 21:42:44 UTC |
| 2dd7ac7 | Scott Smith | 01 October 2012, 21:37:48 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 01 October 2012, 21:37:48 UTC |
| c53ee69 | Scott Smith | 01 October 2012, 21:37:33 UTC | updated display name to show the database ID for solexa/illumina data | 01 October 2012, 21:37:33 UTC |
| e819206 | Malachi Griffith | 01 October 2012, 21:36:19 UTC | Updates needed in clinseq to accommodate upgrades to the somatic-variation and rna-seq pipelines | 01 October 2012, 21:36:19 UTC |
| ca926c2 | Malachi Griffith | 01 October 2012, 21:35:39 UTC | Remove symlinks to test results that had to be removed from the repo | 01 October 2012, 21:35:39 UTC |
| 66c6e75 | Kyung Kim | 01 October 2012, 21:16:51 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 01 October 2012, 21:16:51 UTC |
| ea31b04 | Kyung Kim | 01 October 2012, 21:16:44 UTC | Changed name of default taxonomy_db to reflect the date db was created | 01 October 2012, 21:16:44 UTC |
| 3ca848e | Gabriel Sanderson | 01 October 2012, 21:14:10 UTC | Merge branch 'backfill' into gb_master | 01 October 2012, 21:14:10 UTC |
| 5f6ba6c | Gabriel Sanderson | 25 September 2012, 21:18:33 UTC | Updates for BackfillPolymuttVcf and related modules. Joinx - Add a merge_strategy_file option to pass -M to the binary. Backfill - Region limit before creating the segregating sites file. Dump all workflow xmls. Use SafeVcfMerge for the final merge. Moved vcf header fixing from backfill to RunPolymutt.pm | 01 October 2012, 21:14:04 UTC |
| 6d23fe3 | dmorton | 01 October 2012, 20:59:05 UTC | Remove Data::Dumper from Utility/Text.pm it was unused anyways. | 01 October 2012, 20:59:05 UTC |
| 01b09c7 | dmorton | 01 October 2012, 20:57:18 UTC | Update genome individual show Uses Genome::Utility::List in instead of doing it itself. Shows also any inputs that are delegated (even deeply). | 01 October 2012, 20:58:43 UTC |
| f3ba71a | dmorton | 01 October 2012, 20:55:55 UTC | Return gmb view to old way of showing inputs The other way only works if models behave like builds, and unfortunately some of them don't (it's a problem). | 01 October 2012, 20:58:43 UTC |
| 42c95b7 | Thomas Mooney | 01 October 2012, 19:36:34 UTC | Can't set an error on the object we didn't create. Use the class instead. | 01 October 2012, 19:36:34 UTC |
| 9bab72f | Brian Derickson | 01 October 2012, 16:50:19 UTC | bug fix to Genome::Sys->remove_directory_tree, added comment to test | 01 October 2012, 16:50:19 UTC |
| 9feea73 | Adam Coffman | 01 October 2012, 15:15:48 UTC | increase requested memory for coverage step in rna seq | 01 October 2012, 15:15:48 UTC |
| dab4b1c | Thomas Mooney | 01 October 2012, 13:34:21 UTC | This is what happens when a test diffs against live data. | 01 October 2012, 13:34:21 UTC |
| 3ac8cb9 | APipe Tester | 29 September 2012, 22:44:16 UTC | updated ur submodule to 544ce61 | 29 September 2012, 22:44:16 UTC |
| c9f83bb | Chris Miller | 28 September 2012, 20:53:26 UTC | new tool to query TCGA for UUIDs, add them to a maf, and shift columns accordingly | 28 September 2012, 20:53:38 UTC |
| 20bf0c3 | Ben Oberkfell | 28 September 2012, 20:17:03 UTC | make available version 2.3.2 of varscan | 28 September 2012, 20:17:03 UTC |
| 9774fad | dmorton | 28 September 2012, 17:48:52 UTC | Fix calling gm input show incorrectly. Also put check around terminal size query. | 28 September 2012, 17:48:52 UTC |
| 5e82f85 | dmorton | 28 September 2012, 16:06:27 UTC | Make gmb view show inputs like gm input show | 28 September 2012, 16:07:28 UTC |
| 64f5bf5 | Eddie Belter | 27 September 2012, 22:01:06 UTC | SX: rename input config to params for far, dust and ext cmd base | 27 September 2012, 22:01:28 UTC |
| 5a144f0 | Eddie Belter | 27 September 2012, 21:55:34 UTC | SX: add dust [blast] | 27 September 2012, 22:01:28 UTC |
| 38939cf | Eddie Belter | 27 September 2012, 21:54:41 UTC | SX: return if config does not parse in external cmd base | 27 September 2012, 22:01:27 UTC |
| 6d282e4 | Eddie Belter | 27 September 2012, 21:33:02 UTC | SX: rm test code from external cmd base | 27 September 2012, 22:01:27 UTC |
| 16a1cf8 | Eddie Belter | 27 September 2012, 21:30:10 UTC | SX: add qual file to writer params if exists in external cmd base | 27 September 2012, 22:01:27 UTC |
| e5969c1 | Eddie Belter | 27 September 2012, 20:35:45 UTC | SX: undef input params if writing to cmd input is needed | 27 September 2012, 22:01:26 UTC |
| c338384 | Eddie Belter | 27 September 2012, 20:34:28 UTC | SX: external cmd base returns params for input instead of just files | 27 September 2012, 22:01:26 UTC |
| c7c88fa | Eddie Belter | 27 September 2012, 20:11:50 UTC | SX: Move resolve inputs from FAR to base class ExternalCmdBase | 27 September 2012, 22:01:25 UTC |
| 2917a4e | Eddie Belter | 27 September 2012, 19:26:50 UTC | SX: add type to std in/out reader/writer | 27 September 2012, 22:01:25 UTC |
| 0389402 | Eddie Belter | 27 September 2012, 19:24:46 UTC | SX: add type to sam reader | 27 September 2012, 22:01:25 UTC |
| be9e874 | Eddie Belter | 27 September 2012, 19:23:28 UTC | SX: add type to sff reader | 27 September 2012, 22:01:24 UTC |
| e1318fa | Eddie Belter | 27 September 2012, 19:22:12 UTC | SX: add type to phred reader/writer | 27 September 2012, 22:01:24 UTC |
| 67b6b6f | Eddie Belter | 27 September 2012, 19:19:58 UTC | SX: add type to phred enhanced reader | 27 September 2012, 22:01:24 UTC |
| b23a023 | Eddie Belter | 27 September 2012, 18:52:51 UTC | SX: add type to illumina fastq reader/writer | 27 September 2012, 22:01:23 UTC |
| 3d8793c | Eddie Belter | 27 September 2012, 18:50:44 UTC | SX: add type to fastq reader/writer | 27 September 2012, 22:01:23 UTC |
| f2fc6ce | Eddie Belter | 27 September 2012, 18:48:13 UTC | SX: add type to bam reader | 27 September 2012, 22:01:22 UTC |
| d162442 | Thomas Mooney | 27 September 2012, 21:43:15 UTC | Added libstring-approx-perl to snapshot-deps | 27 September 2012, 21:43:15 UTC |
| d3aec3d | Ben Oberkfell | 27 September 2012, 19:46:33 UTC | change skip file for only new data | 27 September 2012, 19:46:33 UTC |
| 022d7d8 | Ben Oberkfell | 27 September 2012, 19:45:16 UTC | Revert commit to remove accidentally commited change in unrelated file This reverts commit 7c803d735773ad32b57f4d002c857139dea35842. | 27 September 2012, 19:45:16 UTC |
| 7c803d7 | Ben Oberkfell | 27 September 2012, 19:42:23 UTC | change to a new skip file to ensure we sync starting w/ only newly started builds | 27 September 2012, 19:42:32 UTC |
| 83ebe51 | Beifang Niu | 27 September 2012, 19:18:28 UTC | modify code to support VCF format and rearrange help information | 27 September 2012, 19:18:28 UTC |
| 5cb3597 | Travis Abbott | 27 September 2012, 18:50:25 UTC | filter burden summary plots only include things that passed the MAF filter in the burden test | 27 September 2012, 18:51:08 UTC |
| 8deb09a | Feiyu Du | 27 September 2012, 18:17:12 UTC | Remove SOMATIC from Info field | 27 September 2012, 18:17:12 UTC |
| 7ee0ee8 | Charles Lu | 27 September 2012, 18:07:04 UTC | new tool to compare telomere length | 27 September 2012, 18:07:04 UTC |
| c0fecdc | Eddie Belter | 27 September 2012, 18:04:43 UTC | SX: add filters for max Ns and min non Ns | 27 September 2012, 18:04:49 UTC |
| cac9e2f | Christopher C. Harris | 27 September 2012, 17:12:40 UTC | stanky vcfs who need to wash up are now less stanky. fixed DA=1 to be DA=. for new merged vcfs since number of denovo alleleles is no longer capped at one. | 27 September 2012, 17:12:40 UTC |
| 9985f6b | Chris Miller | 27 September 2012, 15:05:45 UTC | adding mm9 as an option | 27 September 2012, 15:05:53 UTC |
| b2844eb | Chris Miller | 27 September 2012, 15:05:12 UTC | added mm9 support | 27 September 2012, 15:05:53 UTC |
| 92663b9 | Cyriac Kandoth | 27 September 2012, 02:20:19 UTC | Support WU format input, and user specified anno DBs | 27 September 2012, 02:20:19 UTC |
| a33a202 | Obi Griffith | 27 September 2012, 01:35:16 UTC | fixed problem with N A Druggable gene category | 27 September 2012, 01:35:16 UTC |
| e45a7dd | Travis Abbott | 26 September 2012, 23:57:42 UTC | make vep reader understand comments | 26 September 2012, 23:58:06 UTC |
| fc2d6f3 | Travis Abbott | 26 September 2012, 23:56:46 UTC | new burden test summary output (phenocorr) We now partition variants into 3 bins in the summary: deleterious and rare deleterious common | 26 September 2012, 23:58:05 UTC |
| 807ff40 | Ben Oberkfell | 26 September 2012, 21:13:57 UTC | Merge branch 'master' of git:/srv/git/genome | 26 September 2012, 21:13:57 UTC |
| d17e483 | Ben Oberkfell | 26 September 2012, 21:13:50 UTC | fix failing test by updating expected status message comparison data | 26 September 2012, 21:13:50 UTC |
| 8d13ee2 | Dan Koboldt | 26 September 2012, 20:52:25 UTC | Revert "Revert "Update VarScan commands to use consistent mpileup -B -q 10 command instead of pileup, and use path_to_jar instead of hard-coded classpath"" This reverts commit 7b07c517d4eb2584ceddab49de0d8bae44b47460. | 26 September 2012, 20:52:25 UTC |
| 2b880ce | Dan Koboldt | 26 September 2012, 20:51:47 UTC | Revert "Revert "Update VarScan commands to use consistent mpileup -B -q 10 command instead of pileup, and use path_to_jar instead of hard-coded classpath"" This reverts commit 02cf5b46fd69a74ed56b682ea6630efff94f3642. | 26 September 2012, 20:51:47 UTC |
| 75fa03f | Anthony Brummett | 26 September 2012, 20:51:34 UTC | Refactor to remove dependancy on Array::Compare Array::Compare has a dependancy on Moose, which we'd rather avoid. The only method it was using was to compare the contents of two lists | 26 September 2012, 20:51:34 UTC |
| 1f301d0 | Jason Walker | 26 September 2012, 20:44:13 UTC | Add a filter for gene biotype to the differential expression in FpkmMatrix | 26 September 2012, 20:45:12 UTC |
| eadbe25 | Eddie Belter | 26 September 2012, 20:43:27 UTC | LIMS/APIPE: rm gsc refs from update genome genotypes | 26 September 2012, 20:43:37 UTC |
| 454e048 | Kyung Kim | 26 September 2012, 20:22:32 UTC | Upate to optionally change taxonomy data base to use | 26 September 2012, 20:22:32 UTC |
| ea5097c | Cyriac Kandoth | 26 September 2012, 20:19:43 UTC | Added option to skip creating a ref-alignment model | 26 September 2012, 20:19:43 UTC |
| a50e43a | Ben Oberkfell | 26 September 2012, 19:56:24 UTC | Merge branch 'master' of git:/srv/git/genome | 26 September 2012, 19:56:24 UTC |
| 02cf5b4 | Ben Oberkfell | 26 September 2012, 19:51:00 UTC | Revert "Update VarScan commands to use consistent mpileup -B -q 10 command instead of pileup, and use path_to_jar instead of hard-coded classpath" This reverts commit 5f0824896210c0b7b6aa9d39e90663d31de16cf2. | 26 September 2012, 19:51:00 UTC |
