| 79d0df9 | Thomas Mooney | 07 January 2014, 15:29:00 UTC | Don't try to summarize an empty splice junction file. | 07 January 2014, 15:29:00 UTC |
| 180ee7a | Avinash Ramu | 06 January 2014, 22:00:01 UTC | remove unwanted test | 06 January 2014, 22:00:01 UTC |
| 0fe180c | Avinash Ramu | 06 January 2014, 21:59:36 UTC | make gmt CnView die if the inputs are invalid | 06 January 2014, 21:59:36 UTC |
| 2523886 | Avinash Ramu | 05 January 2014, 21:30:50 UTC | update expected output to reflect updated name of models: tst1 changed to hcc1395 | 05 January 2014, 21:30:50 UTC |
| 3f98580 | Avinash Ramu | 05 January 2014, 06:04:53 UTC | cleanup function calls | 05 January 2014, 06:04:53 UTC |
| 5a5cf2e | APipe Tester | 04 January 2014, 13:18:27 UTC | Updated `gmt` tab completion. | 04 January 2014, 13:18:27 UTC |
| eac7687 | APipe Tester | 04 January 2014, 13:17:35 UTC | Updated `genome` tab completion. | 04 January 2014, 13:17:35 UTC |
| 595c5cc | Avinash Ramu | 03 January 2014, 23:14:47 UTC | use a seed for cbs segmenter and update microarray-cnv test to use a different chr | 03 January 2014, 23:16:40 UTC |
| 9ec4340 | apregier | 03 January 2014, 22:17:50 UTC | Merge branch 'copy' into gb_master | 03 January 2014, 22:17:50 UTC |
| 4874724 | apregier | 03 January 2014, 22:00:43 UTC | Move list of local properties to a global variable so they are easy to add | 03 January 2014, 22:01:42 UTC |
| 5ba7e5e | apregier | 03 January 2014, 21:57:09 UTC | Move getting args to subroutine | 03 January 2014, 22:01:41 UTC |
| 9a61547 | apregier | 03 January 2014, 21:48:47 UTC | Move getting the cache result to a subroutine | 03 January 2014, 22:01:40 UTC |
| ecd6406 | apregier | 03 January 2014, 21:36:21 UTC | Move more functionality into the subroutine | 03 January 2014, 22:01:40 UTC |
| 4684a5a | apregier | 03 January 2014, 21:31:02 UTC | Move parameter munging to subroutines | 03 January 2014, 22:01:39 UTC |
| 4bd9b85 | apregier | 03 January 2014, 21:12:38 UTC | Move input verification to subroutines for readability | 03 January 2014, 22:01:38 UTC |
| 953d3e6 | Michael J. Kiwala | 02 January 2014, 17:52:34 UTC | handle case when workflow cannot be determined | 03 January 2014, 15:14:16 UTC |
| 1323761 | Michael J. Kiwala | 02 January 2014, 17:11:25 UTC | prevent admin failed-model-tickets from committing Dave Morton and I could not think of reasons why this command should commit | 03 January 2014, 15:14:16 UTC |
| 098d26b | APipe Tester | 03 January 2014, 13:17:19 UTC | Updated `genome` tab completion. | 03 January 2014, 13:17:19 UTC |
| 157bf9f | APipe Tester | 03 January 2014, 13:15:32 UTC | Updated class browser cache. | 03 January 2014, 13:15:32 UTC |
| e4839a6 | Malachi Griffith | 03 January 2014, 04:38:21 UTC | Add check for need to merge split files in file based databases from github | 03 January 2014, 04:38:21 UTC |
| c21068e | Avinash Ramu | 03 January 2014, 03:28:29 UTC | added tool to call CNV's from microarray builds for ClinSeq | 03 January 2014, 03:29:46 UTC |
| 076ebe0 | Adam Coffman | 02 January 2014, 23:34:12 UTC | whitespace | 02 January 2014, 23:34:12 UTC |
| 38d0a7b | Adam Coffman | 02 January 2014, 23:17:26 UTC | update error condition return codes from 0 to undef | 02 January 2014, 23:17:26 UTC |
| b621c0f | Adam Coffman | 02 January 2014, 23:05:32 UTC | Add Genome::Utility::Editor This module allows the user to open an iteractive editor session like `git commit` and returns the contents of the file afterwards. | 02 January 2014, 23:05:32 UTC |
| 8119edb | apregier | 02 January 2014, 22:57:32 UTC | Merge branch 'copy' into gb_master | 02 January 2014, 22:57:32 UTC |
| 981a293 | apregier | 02 January 2014, 22:32:16 UTC | Use api built-in vep script when possible | 02 January 2014, 22:36:39 UTC |
| 8a94ebb | apregier | 02 January 2014, 22:31:11 UTC | Specify which vep script you want | 02 January 2014, 22:36:38 UTC |
| 033c105 | apregier | 02 January 2014, 21:49:25 UTC | Use vep script matching api version where possible | 02 January 2014, 22:34:07 UTC |
| abc8914 | apregier | 02 January 2014, 21:32:34 UTC | The sift/non-sift vep caches are now the same | 02 January 2014, 22:34:06 UTC |
| 4555989 | apregier | 02 January 2014, 21:31:15 UTC | Add vep script download to api software result | 02 January 2014, 22:34:05 UTC |
| 28d205a | apregier | 02 January 2014, 19:37:42 UTC | New versions don't have specific sift/polyphen caches | 02 January 2014, 22:34:04 UTC |
| 7d42242 | Adam Coffman | 02 January 2014, 21:28:33 UTC | add --no-config flag to analysis project create command | 02 January 2014, 21:28:33 UTC |
| 508bef7 | dmorton | 02 January 2014, 20:55:03 UTC | Fix bug preventing --events from working | 02 January 2014, 20:55:52 UTC |
| 36d1598 | Avinash Ramu | 02 January 2014, 20:47:59 UTC | updated the range of x-axis in CnView plots to match the ideogram | 02 January 2014, 20:47:59 UTC |
| 66c0e2c | zskidmor | 02 January 2014, 17:42:28 UTC | Fixed typo | 02 January 2014, 17:42:28 UTC |
| 2fbcfe5 | zskidmor | 02 January 2014, 17:18:43 UTC | Added description | 02 January 2014, 17:18:43 UTC |
| 1f773bf | zskidmor | 02 January 2014, 16:59:22 UTC | fixed typo | 02 January 2014, 16:59:22 UTC |
| 45d6d43 | zskidmor | 02 January 2014, 16:40:48 UTC | added a new tool to compile a matrix of raw counts for rna-seq data and to perform a basic differential expression analysis as an option | 02 January 2014, 16:47:09 UTC |
| f3749ab | APipe Tester | 02 January 2014, 15:22:04 UTC | updated jenkins submodule to 6804680 | 02 January 2014, 15:22:04 UTC |
| ce52475 | Thomas Mooney | 02 January 2014, 14:43:10 UTC | Fix case when only a single model hash is given for a key. | 02 January 2014, 14:43:10 UTC |
| 5c767b0 | APipe Tester | 01 January 2014, 13:17:09 UTC | Updated `genome` tab completion. | 01 January 2014, 13:17:09 UTC |
| 9624180 | APipe Tester | 01 January 2014, 13:15:38 UTC | Updated class browser cache. | 01 January 2014, 13:15:38 UTC |
| e531f0a | Chris Miller | 31 December 2013, 20:10:40 UTC | removing spurious status message when no models are skipped | 31 December 2013, 21:52:46 UTC |
| 82a6d7a | Thomas Mooney | 31 December 2013, 21:31:52 UTC | Fix d8981b50f49d9; remove shadowing "my"s. | 31 December 2013, 21:34:39 UTC |
| 26fe181 | Adam Coffman | 31 December 2013, 21:24:00 UTC | add ShowConfig command for analysis projects | 31 December 2013, 21:24:00 UTC |
| f230183 | Feiyu Du | 31 December 2013, 21:13:32 UTC | update apipe-test-somatic-variation blessed build | 31 December 2013, 21:13:32 UTC |
| c2d50de | Adam Coffman | 31 December 2013, 20:20:41 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 31 December 2013, 20:20:41 UTC |
| 6e67343 | Adam Coffman | 31 December 2013, 20:20:06 UTC | Add CopyConfig command for analysis projects. This command will copy a configuration profile from one analysis project to another. | 31 December 2013, 20:20:06 UTC |
| 5c218dc | apregier | 31 December 2013, 20:19:35 UTC | Merge branch 'copy' into gb_master | 31 December 2013, 20:19:35 UTC |
| 506feb3 | apregier | 31 December 2013, 19:52:28 UTC | Check that all rna-seq builds have the same annotation build input | 31 December 2013, 20:10:17 UTC |
| c0374c2 | apregier | 30 December 2013, 22:53:11 UTC | Add test for unbalanced groups | 31 December 2013, 20:10:16 UTC |
| 2bf68ca | apregier | 30 December 2013, 22:31:03 UTC | Add command for classic edge-r based on rna-seq models | 31 December 2013, 20:10:15 UTC |
| 3658fdc | apregier | 30 December 2013, 21:41:40 UTC | Make MakeGeneCountsFile functionality more generic | 31 December 2013, 20:10:15 UTC |
| 36c50a3 | Malachi Griffith | 31 December 2013, 19:56:19 UTC | add further sanity checks to command for installation of file based databases from github into the standalone gms | 31 December 2013, 19:56:19 UTC |
| 9021d87 | Adam Coffman | 31 December 2013, 19:03:32 UTC | remove unused normalization methods | 31 December 2013, 19:03:32 UTC |
| ec9c5f7 | Malachi Griffith | 31 December 2013, 18:51:41 UTC | Modify hard-coded path to misc-annotation database to use more consistently named version | 31 December 2013, 18:51:41 UTC |
| c68e130 | Nathan Nutter | 31 December 2013, 16:52:59 UTC | hard code to /usr/bin/perl Looks like genome-perl gets setup in the TGI bash profile so we should hard code this hook to /usr/bin/perl. | 31 December 2013, 16:52:59 UTC |
| 7c081f5 | Nathan Nutter | 31 December 2013, 16:47:01 UTC | add status to the default lister fields Since we now have status on allocations, e.g. purged, it makes sense to show this by default. | 31 December 2013, 16:47:01 UTC |
| 0526a5d | Thomas Mooney | 31 December 2013, 14:22:40 UTC | Update test testing strings to match reality. | 31 December 2013, 14:22:40 UTC |
| ed63804 | Thomas Mooney | 31 December 2013, 14:10:17 UTC | Set this to the expected 'genotype file' instead of 'genotype_file'. | 31 December 2013, 14:10:17 UTC |
| 4e37538 | Eddie Belter | 30 December 2013, 23:43:55 UTC | InstData Import: update archive to fastq to use archive::extract | 30 December 2013, 23:56:29 UTC |
| 97b708a | Adam Coffman | 30 December 2013, 21:55:15 UTC | skip merge step if there is only a single file | 30 December 2013, 21:55:15 UTC |
| a357fdf | Adam Coffman | 30 December 2013, 21:55:03 UTC | change to use Genome::Sys->create_symlink | 30 December 2013, 21:55:03 UTC |
| 26c33de | Thomas Mooney | 30 December 2013, 19:55:00 UTC | Update blessed gene-prediction bacterial build. | 30 December 2013, 19:55:00 UTC |
| 1796aa1 | APipe Tester | 30 December 2013, 16:41:29 UTC | updated jenkins submodule to e42e7dd | 30 December 2013, 16:41:29 UTC |
| 608d63c | apregier | 30 December 2013, 16:38:35 UTC | Merge branch 'copy' into gb_master | 30 December 2013, 16:38:35 UTC |
| 71e44f1 | apregier | 30 December 2013, 16:36:08 UTC | Only copy maf file once | 30 December 2013, 16:36:46 UTC |
| 95d1ad0 | Chris Miller | 30 December 2013, 15:58:27 UTC | fixing long indel readcounts from assembly | 30 December 2013, 15:59:51 UTC |
| 97882ca | APipe Tester | 30 December 2013, 14:18:08 UTC | updated workflow submodule to 5986550 | 30 December 2013, 14:18:08 UTC |
| 02c516d | APipe Tester | 28 December 2013, 13:17:07 UTC | Updated `gmt` tab completion. | 28 December 2013, 13:17:07 UTC |
| 5e97c72 | APipe Tester | 28 December 2013, 13:16:24 UTC | Updated `genome` tab completion. | 28 December 2013, 13:16:24 UTC |
| 4eae2ed | APipe Tester | 28 December 2013, 13:14:48 UTC | Updated class browser cache. | 28 December 2013, 13:14:48 UTC |
| 97f0447 | Dave Larson | 27 December 2013, 17:30:38 UTC | Add tool to convert the first sample in a VCF file to bed. | 27 December 2013, 17:30:38 UTC |
| 69da7c1 | APipe Tester | 27 December 2013, 13:18:03 UTC | Updated `gmt` tab completion. | 27 December 2013, 13:18:03 UTC |
| a170641 | APipe Tester | 27 December 2013, 13:17:17 UTC | Updated `genome` tab completion. | 27 December 2013, 13:17:17 UTC |
| cac8d7a | Gabriel Sanderson | 26 December 2013, 22:25:09 UTC | Merge branch 'master' into gb_master | 26 December 2013, 22:25:09 UTC |
| 6eccd55 | Gabriel Sanderson | 26 December 2013, 22:24:07 UTC | Wingspan now has a default of 0, as it is required but was not marked as such | 26 December 2013, 22:24:07 UTC |
| b0e18f0 | Thomas Mooney | 26 December 2013, 20:07:51 UTC | Deduplicate code--call into the Base version. Hopefully one day this might be in a common base class of all three modules that use it, but this seemed better than leaving divergent duplicated code around. | 26 December 2013, 20:07:51 UTC |
| da9e158 | Thomas Mooney | 26 December 2013, 19:51:45 UTC | Consolidate VCF/tabix symlinking into Base | 26 December 2013, 19:51:45 UTC |
| 93035a1 | Thomas Mooney | 26 December 2013, 19:42:24 UTC | Add a true value to the end of the module. | 26 December 2013, 19:42:24 UTC |
| d12e4ed | Thomas Mooney | 26 December 2013, 19:40:42 UTC | Check the existence of the tabix file separately. Otherwise a previously existing result would see the VCF symlink updated but a crash on the tabix symlink. | 26 December 2013, 19:40:42 UTC |
| 67e10ed | Michael J. Kiwala | 26 December 2013, 18:13:42 UTC | upgrade to Git::Repsitory test plugin v.002 * replace File::Temp with calls to new_tmp_repo() * replace install_hook() subroutine with call to install_hook() method | 26 December 2013, 18:19:01 UTC |
| 4786eee | APipe Tester | 26 December 2013, 16:31:29 UTC | updated workflow submodule to 31fe655 | 26 December 2013, 16:31:29 UTC |
| 85b8297 | APipe Tester | 25 December 2013, 13:16:24 UTC | Updated `genome` tab completion. | 25 December 2013, 13:16:24 UTC |
| 1592bdd | APipe Tester | 25 December 2013, 13:14:55 UTC | Updated class browser cache. | 25 December 2013, 13:14:55 UTC |
| e3eb04c | Michael J. Kiwala | 24 December 2013, 18:56:42 UTC | Refactoring pre-receive hook | 24 December 2013, 18:56:42 UTC |
| a46b2e1 | Michael J. Kiwala | 24 December 2013, 15:45:02 UTC | AR-206 pre-receive hook for genome.git Prevents arbitrary users from accidentally stomping on the ur or workflow submodules. | 24 December 2013, 15:46:09 UTC |
| 3c4e41e | Thomas Mooney | 24 December 2013, 15:03:31 UTC | Remove extra whitespace. | 24 December 2013, 15:03:31 UTC |
| 1e8663b | Thomas Mooney | 24 December 2013, 15:02:21 UTC | Remove unneeded manipulation of G:D:Allocation variables. | 24 December 2013, 15:02:21 UTC |
| 9e28931 | Thomas Mooney | 24 December 2013, 14:59:00 UTC | Format the archive time as expected. | 24 December 2013, 14:59:00 UTC |
| 1f2c75a | Thomas Mooney | 24 December 2013, 14:49:27 UTC | Call the accessors directly instead of using nonexistent intermediary. | 24 December 2013, 14:49:27 UTC |
| b25626b | Thomas Mooney | 24 December 2013, 14:42:44 UTC | Remove extra whitespace. | 24 December 2013, 14:43:15 UTC |
| 0127a89 | Thomas Mooney | 24 December 2013, 14:41:34 UTC | Default to now, not 10000 seconds in the future. | 24 December 2013, 14:41:34 UTC |
| 7faf4ea | Thomas Mooney | 24 December 2013, 14:34:24 UTC | Resurrect G:D:C:Allocation::ArchiveExpired This reverts commit d81ef629c6e4e024f3698989770297bee9c1dabd now that AR-89 is resolved. | 24 December 2013, 14:34:24 UTC |
| fb016d5 | Anthony Brummett | 23 December 2013, 21:10:28 UTC | Disable sending email - recepients do not want it anymore | 23 December 2013, 21:10:28 UTC |
| 0e825b6 | Thomas Mooney | 23 December 2013, 19:56:00 UTC | Only process attachments if we have one/some. | 23 December 2013, 19:56:00 UTC |
| c40f082 | Jason Walker | 23 December 2013, 17:21:03 UTC | Remove RNA18S5 and RNA28S5 from the ribosomal protein black list as the genes are now correctly annotated as rRNA genes in Ensembl v74 | 23 December 2013, 17:21:03 UTC |
| 60f42d8 | Malachi Griffith | 22 December 2013, 18:09:21 UTC | Standalone GMS - further fix to command that imports file based databases from github | 22 December 2013, 18:09:21 UTC |
| a279701 | Eddie Belter | 20 December 2013, 22:50:13 UTC | Sx Result: check input count during verify output files | 20 December 2013, 22:50:13 UTC |
| c43b5d6 | Ben Ainscough | 20 December 2013, 19:55:50 UTC | Merge branch 'master' of ssh://git/srv/git/genome Conflicts: lib/perl/Genome/Model/Build/Command/DiffBlessed.pm.YAML | 20 December 2013, 19:55:50 UTC |
