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 |
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 |
7b07c51 | Ben Oberkfell | 26 September 2012, 19:50:43 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 aaa0d7b21259c9c3167f3fc90f394d55ecf585ce. | 26 September 2012, 19:50:43 UTC |
9d75c06 | Adam Coffman | 26 September 2012, 19:23:19 UTC | add missing theme resource for jquery ui | 26 September 2012, 19:23:19 UTC |
29ef6cd | Ben Oberkfell | 26 September 2012, 19:06:34 UTC | Merge branch 'master' of git:/srv/git/genome | 26 September 2012, 19:06:34 UTC |
cddef7c | Ben Oberkfell | 26 September 2012, 19:06:30 UTC | change bwa resource request to use 2 cpus/8gb RAM per APIPE-2437 | 26 September 2012, 19:06:30 UTC |
7b8f213 | apregier | 26 September 2012, 19:05:50 UTC | Merge branch 'allpaths' into gb_master | 26 September 2012, 19:05:50 UTC |
2e3375d | apregier | 26 September 2012, 19:04:50 UTC | New version of allpathslg is available in the command | 26 September 2012, 19:05:18 UTC |
66e2cbf | APipe Tester | 26 September 2012, 18:54:48 UTC | updated ur submodule to 39ea956 | 26 September 2012, 18:54:48 UTC |
db894e2 | APipe Tester | 26 September 2012, 18:52:23 UTC | updated workflow submodule to 4895a84 | 26 September 2012, 18:52:23 UTC |
9a7ac5d | APipe Tester | 26 September 2012, 18:52:22 UTC | updated ur submodule to 3210d77 | 26 September 2012, 18:52:22 UTC |
d622e45 | Jim Weible | 26 September 2012, 18:50:58 UTC | Add tool to dump the dgidb database | 26 September 2012, 18:51:04 UTC |
8ec9246 | Ben Oberkfell | 26 September 2012, 18:46:47 UTC | Merge branch 'master' of git:/srv/git/genome | 26 September 2012, 18:46:47 UTC |
03b0879 | Ben Oberkfell | 26 September 2012, 18:46:36 UTC | update ur submodule | 26 September 2012, 18:46:36 UTC |
e529772 | Thomas Mooney | 26 September 2012, 18:36:23 UTC | Bring the log-parenting to this workflow as well. | 26 September 2012, 18:36:23 UTC |
2a72a51 | Travis Abbott | 26 September 2012, 18:26:04 UTC | remove unused param from BurdenTestSummary maximum_maf is not needed | 26 September 2012, 18:26:47 UTC |
0b38ddc | Dan Koboldt | 26 September 2012, 18:24:00 UTC | Merge branch 'master' of git+ssh://git/srv/git/genome | 26 September 2012, 18:24:00 UTC |
aaa0d7b | Dan Koboldt | 26 September 2012, 18:23:46 UTC | Update VarScan commands to use consistent mpileup -B -q 10 command instead of pileup, and use path_to_jar instead of hard-coded classpath | 26 September 2012, 18:23:46 UTC |
bcc077c | Travis Abbott | 26 September 2012, 18:18:51 UTC | filter variants used in burden summary by MAF | 26 September 2012, 18:19:30 UTC |
5f08248 | Dan Koboldt | 26 September 2012, 18:19:17 UTC | Update VarScan commands to use consistent mpileup -B -q 10 command instead of pileup, and use path_to_jar instead of hard-coded classpath | 26 September 2012, 18:19:17 UTC |
f4c6018 | Dan Koboldt | 26 September 2012, 15:09:31 UTC | New command-line options to let users define rare and deleterious | 26 September 2012, 15:09:31 UTC |
a2b1083 | Ben Oberkfell | 26 September 2012, 03:23:10 UTC | add role tables to postgres mapping | 26 September 2012, 03:23:10 UTC |
c5f2143 | Ben Oberkfell | 26 September 2012, 03:08:09 UTC | remove recursive subclass definition | 26 September 2012, 03:08:09 UTC |
41bac10 | Travis Abbott | 26 September 2012, 02:50:49 UTC | BurdenTestSummary now knows about per-alt vcf entries when using VCF info fields, it is important to remain cognizant of the fact that the standard permits certain fields to apply only to certain alternate alleles. | 26 September 2012, 02:52:52 UTC |
95dec76 | Travis Abbott | 26 September 2012, 02:19:29 UTC | more header validation in Genome::File::Vcf | 26 September 2012, 02:52:52 UTC |
4eefdf8 | Obi Griffith | 26 September 2012, 00:43:05 UTC | Fixed bug in human uniprot check for TTD | 26 September 2012, 00:43:05 UTC |
4f6ee32 | Obi Griffith | 26 September 2012, 00:39:24 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 26 September 2012, 00:39:24 UTC |
ee898de | Obi Griffith | 26 September 2012, 00:38:55 UTC | Further fixes to importers including removal of non-human TTD and Drugbank proteins, improved base_urls, minor nomenclature changes | 26 September 2012, 00:38:55 UTC |
a703656 | Travis Abbott | 25 September 2012, 23:17:12 UTC | add burden test summary for PhenoCor | 25 September 2012, 23:17:35 UTC |
253c28d | Travis Abbott | 25 September 2012, 22:40:35 UTC | add Genome::File::{Vep,Vcf} Vcf will be replaced by Joinx::Vcf perl bindings soon. | 25 September 2012, 23:17:35 UTC |
52ba627 | Malachi Griffith | 25 September 2012, 22:44:36 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 25 September 2012, 22:44:36 UTC |
4b82848 | Malachi Griffith | 25 September 2012, 22:44:18 UTC | Minor bug fixes in automation of clin-seq analysis | 25 September 2012, 22:44:18 UTC |
b460667 | Beifang Niu | 25 September 2012, 22:08:41 UTC | update help infomation | 25 September 2012, 22:08:41 UTC |
deb71c6 | APipe Tester | 25 September 2012, 21:48:41 UTC | updated ur submodule to 3210d77 | 25 September 2012, 21:48:41 UTC |