| 6222a86 | Travis Abbott | 30 March 2013, 00:17:50 UTC | set is_input/is_output on things used as such in workflow | 30 March 2013, 00:17:50 UTC |
| ecad424 | Anthony Brummett | 29 March 2013, 20:50:55 UTC | Add more documentation | 29 March 2013, 21:53:56 UTC |
| 5e189eb | Anthony Brummett | 29 March 2013, 20:50:16 UTC | Don't need File::Compare anymore - we do the comparison ourselves | 29 March 2013, 21:53:56 UTC |
| d9aa135 | Anthony Brummett | 29 March 2013, 20:17:07 UTC | Skip temp vim files to avoid failers when people are looking at them | 29 March 2013, 21:53:55 UTC |
| 02523ef | Anthony Brummett | 29 March 2013, 20:16:09 UTC | Point to a new copy of genome-model-clinseq-update-analysis.out Earlier changes in the branch removed a 'redefined sub' warning - remove it from the expected output | 29 March 2013, 21:53:55 UTC |
| 09bca8b | Anthony Brummett | 26 March 2013, 21:55:48 UTC | This generates tons of output - dump it to /dev/null Check out RT #91254 | 29 March 2013, 21:53:54 UTC |
| e7653bf | Anthony Brummett | 26 March 2013, 21:55:00 UTC | use Sub::Install to avoid 'redefined' warning | 29 March 2013, 21:53:54 UTC |
| c5a24aa | Anthony Brummett | 26 March 2013, 21:54:03 UTC | shellcmd() now accepts redirect_stderr and redirect_stdout params Redirect to a filename | 29 March 2013, 21:53:53 UTC |
| ac45806 | Anthony Brummett | 25 March 2013, 18:45:52 UTC | avoid uninitialized value warnings | 29 March 2013, 21:53:53 UTC |
| 5edf1c3 | Anthony Brummett | 25 March 2013, 16:55:47 UTC | Avoid a warnings from the autoloader by geting the class loaded before calling functions | 29 March 2013, 21:53:52 UTC |
| bcedab2 | Anthony Brummett | 25 March 2013, 16:50:35 UTC | avoid 'redefined' warning | 29 March 2013, 21:53:52 UTC |
| 514b899 | Anthony Brummett | 25 March 2013, 16:42:44 UTC | avoid uninitialized value warning | 29 March 2013, 21:53:51 UTC |
| b3ec050 | Anthony Brummett | 25 March 2013, 16:31:36 UTC | avoid an uninitialized warnings | 29 March 2013, 21:53:51 UTC |
| afc5e44 | Anthony Brummett | 25 March 2013, 16:28:45 UTC | use Sub::Install instead of typeglobs to avoid 'redefined' warnings | 29 March 2013, 21:53:50 UTC |
| 9f88b94 | Anthony Brummett | 25 March 2013, 16:19:23 UTC | avoid uninitialized value warnings | 29 March 2013, 21:53:50 UTC |
| 72a3b46 | Anthony Brummett | 25 March 2013, 16:18:24 UTC | Localize $has_identifiers to avoid an 'earlier declaration' warning | 29 March 2013, 21:53:49 UTC |
| 2f6557b | Ben Oberkfell | 29 March 2013, 21:52:40 UTC | move auth_user to a sensible place so it doesnt cause autoload cycles when loading Genome::Site::TGI | 29 March 2013, 21:52:40 UTC |
| 8054ad7 | Ben Oberkfell | 29 March 2013, 21:51:35 UTC | dont stomp on subroutines with globs | 29 March 2013, 21:51:35 UTC |
| fdeb036 | Ben Oberkfell | 29 March 2013, 19:34:38 UTC | Merge branch 'master' of git:/srv/git/genome | 29 March 2013, 19:34:38 UTC |
| 8da3879 | Ben Oberkfell | 29 March 2013, 19:34:18 UTC | confirm that this is set, not just defined | 29 March 2013, 19:34:18 UTC |
| 00bc1e9 | Chris Miller | 29 March 2013, 17:11:38 UTC | bugfix in quoting names | 29 March 2013, 17:11:52 UTC |
| f11243f | Feiyu Du | 29 March 2013, 15:54:56 UTC | blessing som-var build for new sv annotaion | 29 March 2013, 15:54:56 UTC |
| 81b3c74 | APipe Tester | 29 March 2013, 14:08:40 UTC | updated jenkins submodule to 522c3c1 | 29 March 2013, 14:08:40 UTC |
| c2195b5 | Scott Smith | 28 March 2013, 23:18:01 UTC | show the subject as an object instead of its name, capturing common names, etc. | 28 March 2013, 23:18:01 UTC |
| e32ccf5 | Scott Smith | 28 March 2013, 23:16:06 UTC | Fixed bugs with copying model groups. Changes of params worked, but the following did not: - direct switch of processing profile by ID - changes of inputs declared as is_input - changes of other things (typically inputs declared in legacy way) Now they all do. | 28 March 2013, 23:16:06 UTC |
| fe4b37f | dmorton | 28 March 2013, 23:06:05 UTC | Wrapped change for Flow in if ($ENV{WF_USE_FLOW}) This will fix log files being in unexpected locations. | 28 March 2013, 23:11:44 UTC |
| fbc13ab | APipe Tester | 28 March 2013, 23:11:11 UTC | updated workflow submodule to 40411aa | 28 March 2013, 23:11:11 UTC |
| 1374f70 | APipe Tester | 28 March 2013, 23:11:07 UTC | updated ur submodule to 85edd48 | 28 March 2013, 23:11:07 UTC |
| dbc91fd | Chris Miller | 28 March 2013, 21:32:53 UTC | initial check in of sciclone gmt tool. will write tests soon, as soon as the underlying R package stabilizes (some of these options are going away) | 28 March 2013, 21:32:53 UTC |
| c756be0 | Ian Ferguson | 28 March 2013, 21:09:22 UTC | Fix param parsing for Bwasw | 28 March 2013, 21:09:22 UTC |
| 457a3ce | APipe Tester | 28 March 2013, 20:30:22 UTC | Updated `gmt` tab completion. | 28 March 2013, 20:30:23 UTC |
| 53b05c9 | APipe Tester | 28 March 2013, 20:29:24 UTC | Updated `genome` tab completion. | 28 March 2013, 20:30:23 UTC |
| 0e649d8 | Feiyu Du | 28 March 2013, 20:24:44 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 28 March 2013, 20:24:44 UTC |
| 4bf4ac5 | APipe Tester | 28 March 2013, 20:21:48 UTC | Updated `genome` tab completion. | 28 March 2013, 20:23:07 UTC |
| f0f89e9 | Feiyu Du | 28 March 2013, 20:23:03 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 28 March 2013, 20:23:03 UTC |
| 2df9fca | Feiyu Du | 28 March 2013, 20:21:30 UTC | add detail description to fusion-transcript | 28 March 2013, 20:21:30 UTC |
| 0cae4a4 | nnutter | 28 March 2013, 19:33:27 UTC | ran `ur update classes-from-db` | 28 March 2013, 19:33:46 UTC |
| 7ab2523 | nnutter | 28 March 2013, 19:22:34 UTC | try to complete partially completed refactoring | 28 March 2013, 19:33:46 UTC |
| 6d02648 | Chris Miller | 28 March 2013, 15:50:50 UTC | Added submodule bmm | 28 March 2013, 15:50:50 UTC |
| 03f6fa1 | nnutter | 28 March 2013, 15:34:26 UTC | remove fork, for tracking, at cost of calling a private method | 28 March 2013, 15:34:33 UTC |
| d42b876 | dmorton | 28 March 2013, 15:12:55 UTC | default_tophat_version gives reasonable responses It would previously say that the default was invalid when it clearly is not invalid. | 28 March 2013, 15:14:49 UTC |
| fc536be | dmorton | 26 March 2013, 21:42:50 UTC | Clean up prepare_annotation_index It now uses gmt bio-samtools simulate-rna-seq-reads to make fake_reads Now only supports bowtie2 (legacy support for older bowtie removed) | 28 March 2013, 15:14:49 UTC |
| 14a127a | dmorton | 25 March 2013, 22:11:21 UTC | Add num_transcripts option and fix bug bug: when --nopaired-end is used it still tries to close the file-handle for the reverse reads (which doesn't exist obviously). | 28 March 2013, 15:14:49 UTC |
| 7d557b2 | APipe Tester | 28 March 2013, 15:13:39 UTC | updated jenkins submodule to 9d326a8 | 28 March 2013, 15:13:39 UTC |
| 03ae146 | APipe Tester | 28 March 2013, 14:36:25 UTC | updated jenkins submodule to aea2edf | 28 March 2013, 14:36:25 UTC |
| 7f93b56 | Thomas Mooney | 28 March 2013, 14:26:12 UTC | Override fail_job to increase attempts before giving up. | 28 March 2013, 14:26:12 UTC |
| a32e222 | APipe Tester | 28 March 2013, 05:11:48 UTC | updated ur submodule to f25dca5 | 28 March 2013, 05:11:48 UTC |
| 00959da | Malachi Griffith | 28 March 2013, 02:37:10 UTC | ClinSeq - add date of last analysis to status report on finding complete clinseq analysis using update-analysis | 28 March 2013, 02:37:10 UTC |
| 9b41b17 | Malachi Griffith | 28 March 2013, 02:23:19 UTC | ClinSeq - add additional checks for models that need to be updated in update-analysis | 28 March 2013, 02:23:19 UTC |
| 82b53eb | Malachi Griffith | 28 March 2013, 02:02:37 UTC | ClinSeq - add additional checks for models that need to be updated in update-analysis | 28 March 2013, 02:02:37 UTC |
| 322ef32 | Eddie Belter | 27 March 2013, 22:35:59 UTC | Sample Import: rearrange getting the extraction type | 27 March 2013, 22:36:08 UTC |
| 09bd9c6 | Eddie Belter | 27 March 2013, 22:35:58 UTC | Subject: do not use // when setting nomenclature | 27 March 2013, 22:36:08 UTC |
| ddbe372 | Gabriel Sanderson | 27 March 2013, 22:00:37 UTC | Merge branch 'master' into gb_master | 27 March 2013, 22:00:37 UTC |
| 8a635b5 | Gabriel Sanderson | 27 March 2013, 22:00:02 UTC | do not overwrite default samtools version if the processing profile does not contain one | 27 March 2013, 22:00:17 UTC |
| cd83524 | Eddie Belter | 27 March 2013, 21:48:59 UTC | Sample Import: update configs and tests for incoinsistant naming | 27 March 2013, 21:48:59 UTC |
| 5a47032 | Eddie Belter | 27 March 2013, 21:13:40 UTC | TCGA Bam import: use sample importer | 27 March 2013, 21:13:40 UTC |
| e0e02ac | Eddie Belter | 27 March 2013, 21:08:17 UTC | Sample Import: rm DACC importer, can not find examples that were imported | 27 March 2013, 21:10:15 UTC |
| 98a9b3a | Eddie Belter | 27 March 2013, 21:00:23 UTC | Sample Import: update doc for name | 27 March 2013, 21:10:15 UTC |
| 68eae8d | Eddie Belter | 27 March 2013, 20:48:34 UTC | Sample Import: update help | 27 March 2013, 21:10:15 UTC |
| 5ba05f6 | Eddie Belter | 27 March 2013, 20:28:05 UTC | Sample Import: mv tcga to import.pm | 27 March 2013, 21:10:14 UTC |
| 3faaa0c | Eddie Belter | 27 March 2013, 18:52:00 UTC | Sample Import: mv metahit to import.pm | 27 March 2013, 21:10:14 UTC |
| 6c3c032 | Eddie Belter | 27 March 2013, 18:45:17 UTC | Sample Import: mv embl-ebi to import.pm | 27 March 2013, 21:10:13 UTC |
| ff12e88 | Eddie Belter | 27 March 2013, 18:07:19 UTC | Sample Import: add taxon name to config | 27 March 2013, 21:10:13 UTC |
| 423e4c3 | Eddie Belter | 27 March 2013, 17:55:19 UTC | Sample Import: add fucntionality for same named attributes; add more tests for property metas | 27 March 2013, 21:10:13 UTC |
| 8949c80 | Eddie Belter | 27 March 2013, 17:00:51 UTC | Sample Import: conbine ind name match and sample name match into name_regexp | 27 March 2013, 21:10:12 UTC |
| c53a86e | Eddie Belter | 26 March 2013, 22:12:04 UTC | Sample Import: fix sample/ind attr names; add ATCC namespace | 27 March 2013, 21:10:12 UTC |
| c7ab756 | Eddie Belter | 26 March 2013, 21:56:06 UTC | Sample Import: move nomenclature from base to import | 27 March 2013, 21:10:11 UTC |
| 7f98aa5 | Eddie Belter | 26 March 2013, 21:45:06 UTC | Sample Import: take array or hash for sample/individual attrs | 27 March 2013, 21:10:11 UTC |
| f7a8c72 | Eddie Belter | 26 March 2013, 21:06:36 UTC | Sample Import: extraction type now has default and valid values | 27 March 2013, 21:10:11 UTC |
| 4d476b1 | Eddie Belter | 26 March 2013, 21:01:36 UTC | Sample Import: use one regexp to validate name and get source name; add tests for invalid names | 27 March 2013, 21:10:10 UTC |
| 9564d5b | Eddie Belter | 26 March 2013, 19:10:38 UTC | Sample Import: put import command creation and config loading into methods | 27 March 2013, 21:10:10 UTC |
| 013295e | Eddie Belter | 26 March 2013, 18:42:06 UTC | Sample Import: use entity class to get meta to get properties | 27 March 2013, 21:10:09 UTC |
| e9a3dcc | Eddie Belter | 26 March 2013, 18:36:23 UTC | Sample Import: require nomenclature, derive namespace | 27 March 2013, 21:10:09 UTC |
| 4afea3f | Eddie Belter | 26 March 2013, 18:32:58 UTC | Sample Import: add extraction type "genomic dna" to sample attrs if none set | 27 March 2013, 21:10:09 UTC |
| 3ae1c24 | Eddie Belter | 26 March 2013, 18:30:50 UTC | Sample Import: switch ATCC to use import config | 27 March 2013, 21:10:08 UTC |
| 162e998 | Eddie Belter | 25 March 2013, 22:28:48 UTC | Sample Import: gather all attrs for sample and individual attrs | 27 March 2013, 21:10:08 UTC |
| 4ea1b8c | Eddie Belter | 25 March 2013, 19:41:09 UTC | Sample Import: change sample/ind attrs to names | 27 March 2013, 21:10:07 UTC |
| 87f1fb7 | Eddie Belter | 25 March 2013, 19:30:55 UTC | Sample import: use config to add commands | 27 March 2013, 21:10:07 UTC |
| 0c0e60a | Eddie Belter | 22 March 2013, 21:38:37 UTC | Sample Import: import command generates sub commands for namespaces | 27 March 2013, 21:10:06 UTC |
| 887a308 | Eddie Belter | 22 March 2013, 20:43:09 UTC | Sample Import: update update attrributes | 27 March 2013, 21:10:06 UTC |
| b63725e | Eddie Belter | 22 March 2013, 18:26:59 UTC | Sample Import: add ind and sample attrs to base | 27 March 2013, 21:10:06 UTC |
| ca458f4 | Eddie Belter | 22 March 2013, 17:50:25 UTC | Sample Import: remove _bail method | 27 March 2013, 21:10:05 UTC |
| 2d211ec | Eddie Belter | 22 March 2013, 17:48:38 UTC | Sample Import: removed commits | 27 March 2013, 21:10:05 UTC |
| 3e6c352 | Eddie Belter | 20 March 2013, 22:54:52 UTC | Subject: use bool exp to pull out undeclared attrs; set nomenclature when creating attrs | 27 March 2013, 21:10:04 UTC |
| edad3b6 | Eddie Belter | 20 March 2013, 22:24:31 UTC | Sample: add delete method to delete libraries | 27 March 2013, 21:10:04 UTC |
| 880a2e4 | Malachi Griffith | 27 March 2013, 20:51:12 UTC | Minor update to cn-view figures | 27 March 2013, 20:51:12 UTC |
| e45b94f | Malachi Griffith | 27 March 2013, 20:41:05 UTC | Clin | 27 March 2013, 20:41:05 UTC |
| 542bf94 | Malachi Griffith | 27 March 2013, 20:40:15 UTC | Fix bug to handle ref-align models with now dbsnp build associated | 27 March 2013, 20:40:15 UTC |
| dd4af6e | APipe Tester | 27 March 2013, 20:13:07 UTC | updated jenkins submodule to 2cf8523 | 27 March 2013, 20:13:07 UTC |
| 4ddbf03 | APipe Tester | 27 March 2013, 20:05:03 UTC | updated jenkins submodule to b92b92a | 27 March 2013, 20:05:03 UTC |
| 10c20f6 | APipe Tester | 27 March 2013, 20:02:10 UTC | updated jenkins submodule to da4770c | 27 March 2013, 20:02:10 UTC |
| c41d0ad | APipe Tester | 27 March 2013, 19:33:28 UTC | updated jenkins submodule to ecb044d | 27 March 2013, 19:33:28 UTC |
| 0905421 | APipe Tester | 27 March 2013, 19:33:23 UTC | updated workflow submodule to adde3cf | 27 March 2013, 19:33:23 UTC |
| f4df943 | nnutter | 27 March 2013, 18:31:30 UTC | remove some DRY comments | 27 March 2013, 18:31:49 UTC |
| a7396f3 | nnutter | 27 March 2013, 18:29:58 UTC | simplify test with run_ok | 27 March 2013, 18:31:49 UTC |
| 3d86a14 | nnutter | 27 March 2013, 18:00:37 UTC | improve after test failed due to additional file - Check that we got the expected number of files so it will be clearer if something underneath changed. - Check that the file exists in the $temp_dir. - Check that the file exists in the $expected_output_dir. - Add name to the compare_ok tests. | 27 March 2013, 18:31:48 UTC |
| 26d1c55 | Scott Smith | 27 March 2013, 18:12:25 UTC | lister for current Genome::Db::Base entities | 27 March 2013, 18:12:57 UTC |
| 93abefa | Scott Smith | 26 March 2013, 20:26:01 UTC | test case for htseq results requiring merge of multiple underlying results | 27 March 2013, 18:12:57 UTC |
| 2ea7462 | apregier | 27 March 2013, 16:51:02 UTC | Fix REBUILD option on model define docs test | 27 March 2013, 16:51:02 UTC |
| be17feb | apregier | 27 March 2013, 16:49:59 UTC | Fix expected help output for reference alignment | 27 March 2013, 16:49:59 UTC |
