7d428ea | APipe Tester | 26 October 2013, 12:17:23 UTC | Updated `genome` tab completion. | 26 October 2013, 12:17:23 UTC |
23c5a83 | Ian Ferguson | 25 October 2013, 22:49:10 UTC | Use debug_message in AlignmentResult/Bwasw | 25 October 2013, 22:51:42 UTC |
1a6d979 | Ian Ferguson | 25 October 2013, 22:47:33 UTC | Disconnect dbhandle in AlignmentResult/Bwasw | 25 October 2013, 22:51:42 UTC |
ce5159c | Ian Ferguson | 25 October 2013, 22:04:55 UTC | Add comments to AlignmentResult/Bwasw | 25 October 2013, 22:51:41 UTC |
61a2be8 | APipe Tester | 25 October 2013, 22:30:57 UTC | Updated `genome` tab completion. | 25 October 2013, 22:30:57 UTC |
24c3345 | APipe Tester | 25 October 2013, 22:26:07 UTC | Updated `genome` tab completion. | 25 October 2013, 22:26:07 UTC |
b1d9192 | APipe Tester | 25 October 2013, 22:20:43 UTC | Updated `genome` tab completion. | 25 October 2013, 22:20:43 UTC |
0331c8c | APipe Tester | 25 October 2013, 22:15:59 UTC | Updated `genome` tab completion. | 25 October 2013, 22:15:59 UTC |
b479c07 | APipe Tester | 25 October 2013, 22:11:24 UTC | Updated `genome` tab completion. | 25 October 2013, 22:11:24 UTC |
103c1a7 | APipe Tester | 25 October 2013, 22:06:57 UTC | Updated `gmt` tab completion. | 25 October 2013, 22:06:57 UTC |
73565bb | APipe Tester | 25 October 2013, 22:06:01 UTC | Updated `genome` tab completion. | 25 October 2013, 22:06:01 UTC |
2d4cd88 | APipe Tester | 25 October 2013, 22:04:20 UTC | Updated class browser cache. | 25 October 2013, 22:04:20 UTC |
a896c24 | APipe Tester | 25 October 2013, 22:00:44 UTC | Updated `genome` tab completion. | 25 October 2013, 22:01:41 UTC |
fe8acea | Feiyu Du | 25 October 2013, 21:59:55 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 25 October 2013, 21:59:55 UTC |
887da4b | Feiyu Du | 25 October 2013, 21:56:31 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 25 October 2013, 21:56:31 UTC |
2b3b212 | Feiyu Du | 25 October 2013, 21:56:21 UTC | change to Command::V2 | 25 October 2013, 21:56:21 UTC |
95bbdcb | APipe Tester | 25 October 2013, 21:55:52 UTC | Updated `genome` tab completion. | 25 October 2013, 21:55:52 UTC |
0cf4952 | APipe Tester | 25 October 2013, 21:50:16 UTC | Updated `genome` tab completion. | 25 October 2013, 21:50:16 UTC |
25c5ebc | APipe Tester | 25 October 2013, 21:44:53 UTC | Updated `genome` tab completion. | 25 October 2013, 21:44:53 UTC |
1301823 | APipe Tester | 25 October 2013, 21:39:19 UTC | Updated `genome` tab completion. | 25 October 2013, 21:39:19 UTC |
33f2903 | APipe Tester | 25 October 2013, 21:34:09 UTC | Updated `genome` tab completion. | 25 October 2013, 21:34:09 UTC |
33f833e | APipe Tester | 25 October 2013, 21:28:30 UTC | Updated `genome` tab completion. | 25 October 2013, 21:28:30 UTC |
0797b4a | APipe Tester | 25 October 2013, 21:23:46 UTC | Updated `genome` tab completion. | 25 October 2013, 21:23:46 UTC |
226e9b9 | APipe Tester | 25 October 2013, 19:19:59 UTC | Updated `genome` tab completion. | 25 October 2013, 19:19:59 UTC |
fcd1839 | APipe Tester | 25 October 2013, 19:15:06 UTC | Updated `genome` tab completion. | 25 October 2013, 19:15:06 UTC |
69bcd15 | APipe Tester | 25 October 2013, 19:09:59 UTC | Updated `genome` tab completion. | 25 October 2013, 19:09:59 UTC |
cf4c7b0 | APipe Tester | 25 October 2013, 19:05:08 UTC | Updated `genome` tab completion. | 25 October 2013, 19:05:08 UTC |
03dd413 | APipe Tester | 25 October 2013, 19:00:06 UTC | Updated `genome` tab completion. | 25 October 2013, 19:00:06 UTC |
18fc2f5 | APipe Tester | 25 October 2013, 18:55:16 UTC | Updated `genome` tab completion. | 25 October 2013, 18:55:16 UTC |
39a7d8c | APipe Tester | 25 October 2013, 18:50:27 UTC | Updated `genome` tab completion. | 25 October 2013, 18:50:27 UTC |
1ac06ef | Ben Ainscough | 25 October 2013, 18:29:08 UTC | updated version of circos | 25 October 2013, 18:29:08 UTC |
bcabbc1 | Jasreet Hundal | 25 October 2013, 17:00:37 UTC | Updated help | 25 October 2013, 17:00:37 UTC |
d921f2e | APipe Tester | 25 October 2013, 11:19:10 UTC | Updated `genome` tab completion. | 25 October 2013, 11:19:10 UTC |
766d01b | APipe Tester | 25 October 2013, 06:05:47 UTC | Updated `genome` tab completion. | 25 October 2013, 06:05:47 UTC |
55132dc | Nathan Nutter | 25 October 2013, 01:51:02 UTC | looks like a bunch of things got renamed to tst1 | 25 October 2013, 01:52:20 UTC |
0efc99d | Adam Coffman | 24 October 2013, 23:43:19 UTC | purging should set kb_{used,requested} to 0 | 24 October 2013, 23:43:19 UTC |
f89a011 | Thomas Mooney | 24 October 2013, 22:23:25 UTC | Skip any parts that don't point to valid entities. | 24 October 2013, 22:23:25 UTC |
949d7a4 | Ben Ainscough | 24 October 2013, 22:12:27 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 24 October 2013, 22:12:27 UTC |
914bf35 | Ben Ainscough | 24 October 2013, 22:11:01 UTC | updated regex for snvs and indels to be more robust | 24 October 2013, 22:11:01 UTC |
acf5f5e | APipe Tester | 24 October 2013, 22:10:31 UTC | Updated `gmt` tab completion. | 24 October 2013, 22:10:31 UTC |
a075fca | APipe Tester | 24 October 2013, 22:09:43 UTC | Updated `genome` tab completion. | 24 October 2013, 22:09:43 UTC |
a885235 | APipe Tester | 24 October 2013, 22:07:54 UTC | Updated class browser cache. | 24 October 2013, 22:07:54 UTC |
d397a9e | Nathan Nutter | 24 October 2013, 20:32:50 UTC | remove skip over symlinks | 24 October 2013, 22:00:39 UTC |
7287c97 | Nathan Nutter | 24 October 2013, 21:52:53 UTC | looks like a bunch of things got renamed to tst1 | 24 October 2013, 21:52:53 UTC |
9ac9f8e | Adam Coffman | 24 October 2013, 21:01:55 UTC | add ability to purge allocations | 24 October 2013, 21:01:55 UTC |
eec4e49 | Adam Coffman | 24 October 2013, 19:14:12 UTC | add create_file_summaries method to allocations | 24 October 2013, 19:14:12 UTC |
743d016 | Mark Burnett | 24 October 2013, 19:01:29 UTC | make `genome search` to be more like web search | 24 October 2013, 19:05:03 UTC |
6b98e84 | APipe Tester | 24 October 2013, 19:04:13 UTC | updated jenkins submodule to 9443f13 | 24 October 2013, 19:04:13 UTC |
2c219d9 | Adam Coffman | 24 October 2013, 18:52:57 UTC | add create_or_update method | 24 October 2013, 18:52:57 UTC |
5150d7a | Chris Miller | 24 October 2013, 18:28:23 UTC | adding somvar option | 24 October 2013, 18:28:53 UTC |
6fc1c0a | Adam Coffman | 24 October 2013, 18:23:40 UTC | add file summary objects to prepare for allocation purging | 24 October 2013, 18:23:40 UTC |
33cb819 | Nathan Nutter | 24 October 2013, 15:34:10 UTC | rm metric: disk.allocation.create.get_allocation_without_lock.selection Removed metric, disk.allocation.create.get_allocation_without_lock.selection, because it, more-or-less, completely overlapped another metric, disk.allocation.create.get_allocation_without_lock. | 24 October 2013, 15:34:10 UTC |
c04fdc2 | Nathan Nutter | 24 October 2013, 14:30:57 UTC | add metric: disk.allocation.get_allocation_without_lock.rollback.over_used | 24 October 2013, 14:31:08 UTC |
3ee59e8 | Nathan Nutter | 24 October 2013, 14:30:35 UTC | add metric: disk.allocation.get_allocation_without_lock.rollback.over_allocated | 24 October 2013, 14:31:07 UTC |
286660a | APipe Tester | 24 October 2013, 14:25:52 UTC | Updated `genome` tab completion. | 24 October 2013, 14:25:52 UTC |
2fc7533 | Thomas Mooney | 24 October 2013, 13:37:38 UTC | Update the blessed build due to new fgenesh version. | 24 October 2013, 13:37:38 UTC |
8538776 | APipe Tester | 24 October 2013, 11:28:06 UTC | Updated `genome` tab completion. | 24 October 2013, 11:28:06 UTC |
3a1120f | APipe Tester | 24 October 2013, 11:26:29 UTC | Updated class browser cache. | 24 October 2013, 11:26:29 UTC |
3ad0fbd | Gabriel Sanderson | 23 October 2013, 23:32:16 UTC | Merge branch 'varscanparam' into gb_master | 23 October 2013, 23:32:16 UTC |
76a9ef9 | Gabriel Sanderson | 23 October 2013, 23:26:10 UTC | Corrected a bug that prevented baq from being turned off with --nobaq | 23 October 2013, 23:31:25 UTC |
684ca89 | Gabriel Sanderson | 23 October 2013, 23:06:06 UTC | Expanded VarscanBase test | 23 October 2013, 23:31:24 UTC |
b5f8e69 | Gabriel Sanderson | 23 October 2013, 22:40:52 UTC | Move has_version into VarscanBase | 23 October 2013, 23:31:23 UTC |
ac67136 | Gabriel Sanderson | 23 October 2013, 22:37:52 UTC | DV2 Varscan modules inherit from VarscanBase and _process_samtools_params and _split_params are moved up. | 23 October 2013, 23:31:23 UTC |
738bdf9 | Gabriel Sanderson | 23 October 2013, 22:33:28 UTC | Added VarscanBase | 23 October 2013, 23:31:22 UTC |
d12468a | Gabriel Sanderson | 23 October 2013, 22:29:51 UTC | Enable samtools parameter processing in VarscanSomaticValidation (previously only worked in Varscan germline) | 23 October 2013, 23:31:21 UTC |
f6dfd6a | Gabriel Sanderson | 23 October 2013, 22:25:58 UTC | Enable samtools parameter processing in VarscanSomatic (previously only worked in Varscan germline) | 23 October 2013, 23:31:21 UTC |
9d261f0 | Nathan Nutter | 23 October 2013, 22:50:10 UTC | allow expected/got count to be shown in diag | 23 October 2013, 23:12:09 UTC |
7fe1c6b | Nathan Nutter | 23 October 2013, 22:26:35 UTC | extract method: _existing_allocation_path_check | 23 October 2013, 23:12:08 UTC |
35a13e1 | Nathan Nutter | 23 October 2013, 22:14:15 UTC | add metric: disk.allocation.require | 23 October 2013, 23:12:07 UTC |
5ec72bf | Nathan Nutter | 23 October 2013, 21:58:39 UTC | add metric: disk.allocation.get_parent_allocation | 23 October 2013, 23:12:07 UTC |
59b8b0e | Nathan Nutter | 23 October 2013, 21:54:25 UTC | add metric: disk.allocation.child_allocation_query | 23 October 2013, 23:12:05 UTC |
b163ec2 | Nathan Nutter | 23 October 2013, 21:42:21 UTC | push existing allocation_path down to _get_allocation_without_lock Checking that an allocation_path does not exist on every candidate volume is very slow due to having to mount the volume and stat a path. This pushes the check down to where each candidate volume is attempted rather than checking all candidate volumes. | 23 October 2013, 23:12:04 UTC |
8062269 | Nathan Nutter | 23 October 2013, 21:51:48 UTC | fix old typo | 23 October 2013, 23:12:03 UTC |
ecc5101 | APipe Tester | 23 October 2013, 21:44:45 UTC | Updated `genome` tab completion. | 23 October 2013, 21:44:45 UTC |
010637b | APipe Tester | 23 October 2013, 21:43:14 UTC | Updated class browser cache. | 23 October 2013, 21:43:14 UTC |
37d1a20 | Mark Burnett | 23 October 2013, 18:57:01 UTC | make search work for multiple results | 23 October 2013, 21:05:23 UTC |
4bd0453 | Mark Burnett | 23 October 2013, 15:00:03 UTC | display single and many differently | 23 October 2013, 21:05:23 UTC |
d91a3e2 | Mark Burnett | 23 October 2013, 14:07:30 UTC | update low score warning message | 23 October 2013, 21:05:22 UTC |
ae63819 | Mark Burnett | 23 October 2013, 14:00:07 UTC | add basic model shower | 23 October 2013, 21:05:22 UTC |
baed53f | Mark Burnett | 22 October 2013, 21:18:58 UTC | rename `genome show` to `genome search` | 23 October 2013, 21:05:21 UTC |
29ebf0b | Mark Burnett | 22 October 2013, 15:23:24 UTC | complete sketch of show command | 23 October 2013, 21:05:21 UTC |
175f9e6 | Mark Burnett | 22 October 2013, 14:22:35 UTC | add show to Genome::Command | 23 October 2013, 21:05:20 UTC |
f408635 | Mark Burnett | 22 October 2013, 14:22:10 UTC | sort subcommands in Genome::Command | 23 October 2013, 21:05:20 UTC |
2f2fe27 | Mark Burnett | 22 October 2013, 14:21:42 UTC | whitespace | 23 October 2013, 21:05:19 UTC |
927321d | Mark Burnett | 22 October 2013, 14:21:12 UTC | add empty Show command | 23 October 2013, 21:05:18 UTC |
bf1a5df | Thomas Mooney | 23 October 2013, 20:10:19 UTC | Update path since new version installed or... Trade one hardcoded path for another | 23 October 2013, 20:10:19 UTC |
2c33e65 | APipe Tester | 23 October 2013, 18:55:52 UTC | Updated `genome` tab completion. | 23 October 2013, 18:55:52 UTC |
b3df6a6 | Thomas Mooney | 23 October 2013, 18:46:18 UTC | Add support for updating other kinds of projects with the new models. (Other kinds of projects means anything currently a Genome::Project monitoring that instrument data.) | 23 October 2013, 18:48:30 UTC |
4dd4497 | APipe Tester | 23 October 2013, 18:35:30 UTC | Updated `genome` tab completion. | 23 October 2013, 18:35:30 UTC |
80d4126 | APipe Tester | 23 October 2013, 18:33:56 UTC | Updated class browser cache. | 23 October 2013, 18:33:56 UTC |
01af232 | Thomas Mooney | 23 October 2013, 16:18:00 UTC | New command to update model membership in projects based on existing parts. | 23 October 2013, 16:18:00 UTC |
d631ec9 | Thomas Mooney | 23 October 2013, 16:17:23 UTC | If get parts is an instance method, it should get parts for that instance! | 23 October 2013, 16:17:23 UTC |
119d5bc | Thomas Mooney | 23 October 2013, 15:14:09 UTC | Add a space between the name and ID. | 23 October 2013, 15:14:09 UTC |
c43fa2d | APipe Tester | 23 October 2013, 11:27:11 UTC | Updated `genome` tab completion. | 23 October 2013, 11:27:11 UTC |
328112c | Adam Coffman | 22 October 2013, 22:17:30 UTC | require analysis project in order to sync over from lims | 22 October 2013, 22:17:30 UTC |
0b52e9d | Nathan Nutter | 22 October 2013, 22:12:54 UTC | add metric: disk.allocation.create.get_allocation_without_lock.selection | 22 October 2013, 22:12:54 UTC |
5a06289 | Nathan Nutter | 22 October 2013, 22:12:28 UTC | add metric: disk.allocation.create.create_directory | 22 October 2013, 22:12:28 UTC |
a21d471 | Nathan Nutter | 22 October 2013, 22:11:52 UTC | add metric: disk.allocation.create.get_allocation_without_lock | 22 October 2013, 22:11:52 UTC |
aadbb2a | Nathan Nutter | 22 October 2013, 22:11:30 UTC | add metric: disk.allocation.create.candidate_volumes.existing_allocation_path_check | 22 October 2013, 22:11:30 UTC |
2dfb084 | Nathan Nutter | 22 October 2013, 22:10:57 UTC | add metric: disk.allocation.create.candidate_volumes.selection | 22 October 2013, 22:10:57 UTC |