| HEAD | 696b1e7 | Merge pull request #2077 from tmooney/retry_connections Retry postgres connections for up to 90 seconds. | 13 March 2024, 13:58:29 UTC |
| refs/for/master | 48a14df | whitespace Change-Id: Ib79e43576f28e3f097e851469d805f160a0a1562 | 01 November 2012, 19:20:14 UTC |
| refs/heads/chrisamiller-patch-1 | 82d230a | preserve "build" prefix on build directory name the rest of gms uses a "build" prefix, this should too, for consistency (especially during storage1 migration) | 07 February 2020, 18:49:32 UTC |
| refs/heads/cle | 43e9827 | Merge pull request #299 from apregier/fix_caf_doc Fix documentation string for caf | 09 December 2014, 22:09:14 UTC |
| refs/heads/cle-snapshot | c14eeb1 | Use simpler means of validating LSF queue. Idea borrowed from Genome::ConfigValidator::LSFQueue. That module cannot "use Genome;" so can't be changed to refer to this version instead. | 28 February 2017, 16:51:50 UTC |
| refs/heads/cle-staging | d43ba15 | Merge pull request #1658 from dufeiyu/qc_error_rate Try to get error_rate from Genome::Qc::Result metrics | 02 February 2017, 20:12:48 UTC |
| refs/heads/cram | 80bbd1a | cleaner status messages | 13 August 2019, 20:18:15 UTC |
| refs/heads/cwltool-path | 02746a6 | updating cwltool path path changed in more recent docker versions | 26 July 2021, 18:57:01 UTC |
| refs/heads/gms-pub | a6614cf | Fix defaults for SGMS | 30 November 2015, 23:31:13 UTC |
| refs/heads/gms-pub-2015.02.22 | 6a77af3 | Merge pull request #527 from gatoravi/site-config configure a site module for the SGMS. | 04 March 2015, 22:06:35 UTC |
| refs/heads/gms-pub-2015.03.04 | fb45df7 | Merge pull request #676 from gatoravi/fix_build_email SGMS: configure email addresses for build reports. | 21 April 2015, 20:21:42 UTC |
| refs/heads/gms-pub-before-plos-merge-from-master | cb10fc3 | check for genotype microarray processing profile input_format instead of genotype microarray processing profile name | 30 September 2014, 16:36:49 UTC |
| refs/heads/gotcloud | 3ce1ad8 | changed requirement for anno/refbuild | 13 August 2014, 20:58:15 UTC |
| refs/heads/master | 696b1e7 | Merge pull request #2077 from tmooney/retry_connections Retry postgres connections for up to 90 seconds. | 13 March 2024, 13:58:29 UTC |
| refs/heads/mcallawa_trusty | b77d952 | Do not build an LSF resource requirement for 'inline' mode. | 14 April 2015, 17:16:34 UTC |
| refs/heads/model-tests | 696b1e7 | Merge pull request #2077 from tmooney/retry_connections Retry postgres connections for up to 90 seconds. | 13 March 2024, 13:58:29 UTC |
| refs/heads/model-tests-for-lsf9 | 91d94fd | Another variable gone... | 24 July 2015, 20:09:44 UTC |
| refs/heads/perl-tests | 696b1e7 | Merge pull request #2077 from tmooney/retry_connections Retry postgres connections for up to 90 seconds. | 13 March 2024, 13:58:29 UTC |
| refs/heads/revert-606-gmt_picard_typos | 3d32d95 | Revert "Fix gmt picard typos; remove duplicate method" | 01 April 2015, 20:31:47 UTC |
| refs/heads/snapshot | 696b1e7 | Merge pull request #2077 from tmooney/retry_connections Retry postgres connections for up to 90 seconds. | 13 March 2024, 13:58:29 UTC |
| refs/tags/AP-103 | eff63c7 | Remove cached reference alignments from DV2. | 03 October 2013, 19:32:53 UTC |
| refs/tags/genome-3177 | 43d0567 | Improved usage example for Entrez Importer | 16 September 2012, 23:05:10 UTC |
| refs/tags/genome-3178 | 5979329 | Merge branch 'master' of ssh://git/srv/git/genome | 18 September 2012, 16:43:14 UTC |
| refs/tags/genome-3179 | f4d4c68 | Numerous fixes and updates to importers | 19 September 2012, 00:34:17 UTC |
| refs/tags/genome-3180 | 0bbb52e | Microarray Extract: update snp id column setting b/c of swithc to switch to 137 | 19 September 2012, 18:35:57 UTC |
| refs/tags/genome-3181 | e756450 | GMT LIMS APIPE: rename fix pidfa params to fir pse params; update class info and help | 19 September 2012, 20:09:47 UTC |
| refs/tags/genome-3182 | 2d664d0 | Define the merged transcript gtf file path for cuffmerge. | 19 September 2012, 21:04:20 UTC |
| refs/tags/genome-3183 | 8cfa505 | CHANGELOG: AQID - NO MORE QIDFGM REFS! | 19 September 2012, 23:21:47 UTC |
| refs/tags/genome-3184 | 26f917a | Merge branch 'updated' into gb_master | 20 September 2012, 15:54:24 UTC |
| refs/tags/genome-3185 | ad29987 | fix use statement for Genome::Utility::Vcf | 20 September 2012, 16:08:41 UTC |
| refs/tags/genome-3186 | a8ec08b | Merge branch 'updated' into gb_master | 20 September 2012, 19:05:54 UTC |
| refs/tags/genome-3187 | 16e652b | Merge branch 'updated' into gb_master | 20 September 2012, 20:45:00 UTC |
| refs/tags/genome-3188 | 9781e8c | new version of pairoscope for deploy | 20 September 2012, 21:59:23 UTC |
| refs/tags/genome-3189 | 5ec75cc | Finished first complete version of clinseq update-analysis | 21 September 2012, 02:44:57 UTC |
| refs/tags/genome-3190 | d49f555 | Add significant gene heatmap | 21 September 2012, 14:35:01 UTC |
| refs/tags/genome-3191 | a043f89 | Fixed clin-seq test cases that were failing do to database updates that changed the results of some queries | 24 September 2012, 03:59:08 UTC |
| refs/tags/genome-3192 | 92663b9 | Support WU format input, and user specified anno DBs | 27 September 2012, 02:20:19 UTC |
| refs/tags/genome-3194 | dab4b1c | This is what happens when a test diffs against live data. | 01 October 2012, 13:34:21 UTC |
| refs/tags/genome-3196 | 9feea73 | increase requested memory for coverage step in rna seq | 01 October 2012, 15:15:48 UTC |
| refs/tags/genome-3197 | 6d23fe3 | Remove Data::Dumper from Utility/Text.pm it was unused anyways. | 01 October 2012, 20:59:05 UTC |
| refs/tags/genome-3198 | 9e541bf | Merge branch 'master' of ssh://git/srv/git/genome | 01 October 2012, 22:05:40 UTC |
| refs/tags/genome-3199 | f0b02ea | Merge branch 'master' of ssh://git/srv/git/genome | 02 October 2012, 15:20:45 UTC |
| refs/tags/genome-3200 | 259f15f | add picard 1.77 as an available version | 02 October 2012, 20:49:00 UTC |
| refs/tags/genome-3201 | 78c758e | assign (un)archive to a job group | 03 October 2012, 21:04:15 UTC |
| refs/tags/genome-3202 | 6c2e59a | Revert all statsd client code. This reverts commits: 6c614a5541335a9886f57d6b2c136938c52a5888 3709183628244f00805ce7e95aca1fb938067491 ede989d6c7c47d4842bce499450c2bbc6ffb68bc 8285ce9c889cd2412c06fedefc7964d7f7dd6b66 80c40f6d23b561f781184c312ba775240997c858 f679cd1b1942e9c2dc735e8ebc6ac253a54e61ac Must wait until perl 5.8 dependency is installed. | 09 October 2012, 20:19:57 UTC |
| refs/tags/genome-3203 | 97b623b | gmb view now shows logs of running steps | 09 October 2012, 23:00:13 UTC |
| refs/tags/genome-3204 | 585444d | add some code to display genomic control and standard error | 10 October 2012, 02:54:21 UTC |
| refs/tags/genome-3206 | 4baccbd | Add a none option to skip coverage | 09 October 2012, 14:25:35 UTC |
| refs/tags/genome-3207 | d885297 | Merge branch 'fireteam' into gb_master | 10 October 2012, 16:41:53 UTC |
| refs/tags/genome-3209 | e62665e | Merge branch 'master' of ssh://git/srv/git/genome | 10 October 2012, 17:09:16 UTC |
| refs/tags/genome-3210 | add9d91 | add rs id to test to double check implementation. Still vulnerable to changes to clinical correlation | 10 October 2012, 21:05:12 UTC |
| refs/tags/genome-3211 | 161364e | removed samtools (used just as a prefilter for and thus redundant with sniper) | 11 October 2012, 00:13:24 UTC |
| refs/tags/genome-3212 | 92a75b8 | Reintroduce use of previously discovered variants into default clin-seq processing steps | 11 October 2012, 00:41:46 UTC |
| refs/tags/genome-3214 | 166530e | removed virome-event cd-hit remove files workflow event | 11 October 2012, 15:21:14 UTC |
| refs/tags/genome-3215 | 1f3e827 | updated workflow submodule to 6d2e351 | 11 October 2012, 15:39:06 UTC |
| refs/tags/genome-3216 | 3e38301 | update data_directory test to only care about allocation_path portion | 11 October 2012, 20:20:33 UTC |
| refs/tags/genome-3217 | bf01b62 | 4 column ROI files can now be used with annotation-format | 11 October 2012, 22:53:59 UTC |
| refs/tags/genome-3218 | 9ff1a67 | updated workflow submodule to f8d15b1 | 12 October 2012, 02:18:56 UTC |
| refs/tags/genome-3219 | 6fde969 | Revert the value_class_name to Genome::Model::ReferenceAlignment for tumor and normal models in SomaticVariation. The value_class_name is used when inputs are defined. Another solution will be reaquired so Genome::Model::RnaSeq is a valid model class. | 12 October 2012, 21:39:28 UTC |
| refs/tags/genome-3220 | cc95713 | Merge branch 'master' of ssh://git/srv/git/genome | 12 October 2012, 22:19:55 UTC |
| refs/tags/genome-3221 | 9418daf | Fix chrom bounds exception, and add option to print reading frames | 15 October 2012, 12:37:29 UTC |
| refs/tags/genome-3222 | 87eb4f3 | Merge branch 'music' into gb_master | 15 October 2012, 14:53:27 UTC |
| refs/tags/genome-3223 | 26d8306 | Minor update to clinseq to allow samples combined from multiple individuals by use of --force | 15 October 2012, 17:49:54 UTC |
| refs/tags/genome-3224 | cda533a | Merge branch 'my_annotation' into gb_master | 15 October 2012, 18:42:35 UTC |
| refs/tags/genome-3225 | 6ddb387 | archiving now checks file permissions before attempting to archive | 15 October 2012, 22:30:13 UTC |
| refs/tags/genome-3226 | 5daf177 | Allow incompatible references for RNASeq instrument data that will be aligned. | 16 October 2012, 16:11:28 UTC |
| refs/tags/genome-3227 | a05bc35 | do FET for genes with rare+deleterious variants | 16 October 2012, 17:34:38 UTC |
| refs/tags/genome-3228 | f4d5b03 | force symlink creation over existing destination | 16 October 2012, 18:35:36 UTC |
| refs/tags/genome-3229 | c5bfb9e | updated ur submodule to bb913e1 | 17 October 2012, 21:48:22 UTC |
| refs/tags/genome-3230 | 30e1a2f | adding indel readcounts | 15 October 2012, 15:08:23 UTC |
| refs/tags/genome-3231 | c53d290 | Merge branch 'vep' into gb_master | 18 October 2012, 21:10:11 UTC |
| refs/tags/genome-3232 | f903bde | tMerge branch 'master' of ssh://git/srv/git/genome | 18 October 2012, 21:25:21 UTC |
| refs/tags/genome-3233 | 50249b3 | fixed null in-clause warning In Genome::Model::Build::ReferenceAlignment->merged_alignment_result, should only attempt to get merged alignment results if any software result users that point to the current build are found. If none are found, just return immediately. Before this change, a Genome::InstrumentData::AlignmentResult::Merged->get(undef) was performed, which emitted a warning and always returned nothing. | 19 October 2012, 19:00:53 UTC |
| refs/tags/genome-3234 | 4f4aa3d | update submodule pointer: genome-snapshot-deps | 19 October 2012, 21:51:09 UTC |
| refs/tags/genome-3235 | f9fc45c | consider all genes in which a variant is deleterious The rare/deleterious test previously only used the most severe gene. | 22 October 2012, 21:23:32 UTC |
| refs/tags/genome-3236 | e0b6662 | updated workflow submodule to dc6b73c | 23 October 2012, 02:37:47 UTC |
| refs/tags/genome-3237 | 10c14cf | bug fix .. remove existing parse output file to prevent it from crashing when using g::sys->open_file_for_writing to write new parse file during re-runs | 23 October 2012, 15:40:13 UTC |
| refs/tags/genome-3238 | 78e32a6 | updated workflow submodule to cba0eaa | 23 October 2012, 16:28:37 UTC |
| refs/tags/genome-3239 | 1963ac6 | Enhance 'genome model build status' Now shows model id in addition to model name. Now has color option for statuses. | 24 October 2012, 15:36:49 UTC |
| refs/tags/genome-3240 | b84fdb2 | Solexa: update gettign default results | 24 October 2012, 16:30:16 UTC |
| refs/tags/genome-3241 | 9fca9f4 | Add Total (reads) to report. | 24 October 2012, 18:59:49 UTC |
| refs/tags/genome-3242 | a7a2ab6 | Fix Sys.pm to output more sensible error message. Now resets $! before executing cmd so that old "No such file or directory" errors aren't reported as comming from this cmd. | 24 October 2012, 19:33:54 UTC |
| refs/tags/genome-3243 | 9ed9e7f | updated workflow submodule to cd937bf | 24 October 2012, 20:47:14 UTC |
| refs/tags/genome-3244 | 80960a5 | Whitespace only | 24 October 2012, 21:55:46 UTC |
| refs/tags/genome-3245 | 845720e | Merge branch 'master' of ssh://git/srv/git/genome :( | 25 October 2012, 14:13:58 UTC |
| refs/tags/genome-3246 | 43b976a | Wrap Instrumentation::timing with eval | 25 October 2012, 14:34:24 UTC |
| refs/tags/genome-3247 | e4eed3f | Merge branch 'master' of ssh://git/srv/git/genome | 25 October 2012, 18:40:49 UTC |
| refs/tags/genome-3248 | e74b04b | Merge branch 'music' into gb_master | 25 October 2012, 19:25:32 UTC |
| refs/tags/genome-3249 | c0ef9af | Minor updates to clinseq analysis setup | 27 October 2012, 14:46:39 UTC |
| refs/tags/genome-3250 | 7a474d7 | changed filtering to be based on chromosome and position only. Should make it more robust to changes to the ends of ids. | 29 October 2012, 15:20:44 UTC |
| refs/tags/genome-3253 | 676b3c6 | update test data to match expected results the previous test data was asserting that the code did the wrong thing (passed files to joinx in incorrect order due to filenames being hashed then iterating over the keys). | 01 November 2012, 21:02:21 UTC |
| refs/tags/genome-3254 | e01e5ba | updated jenkins submodule to 0d2f07b | 02 November 2012, 14:16:32 UTC |
| refs/tags/genome-3255 | ad7a859 | Merge remote-tracking branch 'origin/master' | 02 November 2012, 19:12:09 UTC |
| refs/tags/genome-3257 | 05b466e | Merge remote-tracking branch 'origin/master' | 02 November 2012, 20:08:38 UTC |
| refs/tags/genome-3258 | d6be815 | fix uninitialized warning for exclude_mount_path | 03 November 2012, 02:11:35 UTC |
| refs/tags/genome-3259 | f3e0a82 | Testing with live data continues to make us cry. Update expected results. | 08 November 2012, 14:08:38 UTC |
| refs/tags/genome-3260 | d754ca1 | change the description of format FT to be TCGA-compliant | 09 November 2012, 17:27:59 UTC |
| refs/tags/genome-3261 | 2335512 | add optional --file-suffix option to gmt graph mutation-diagram | 12 November 2012, 23:33:22 UTC |
| refs/tags/genome-3262 | 5b194f9 | updated jenkins submodule to 6dbe3a7 | 14 November 2012, 21:32:50 UTC |
| refs/tags/genome-3263 | b45e640 | working on adding segments to CnView analysis | 15 November 2012, 00:58:15 UTC |
