1260120 | Chris Miller | 28 August 2013, 21:59:26 UTC | revamped tool to work on newer file formats instead of just using Varscan input | 28 August 2013, 22:00:03 UTC |
d27817f | APipe Tester | 28 August 2013, 19:40:11 UTC | Updated `genome` tab completion. | 28 August 2013, 19:40:11 UTC |
405928a | APipe Tester | 28 August 2013, 19:38:14 UTC | Updated class browser cache. | 28 August 2013, 19:38:14 UTC |
199db77 | Feiyu Du | 28 August 2013, 19:28:45 UTC | Add AnnotateGenesByDgidb.pm to ClinSeq | 28 August 2013, 19:29:43 UTC |
d17f841 | Travis Abbott | 28 August 2013, 19:02:31 UTC | make gmt instrument-data import bam return 0/1 it was returning an instrument data id, and command v1 was expecting a number | 28 August 2013, 19:02:31 UTC |
4030736 | APipe Tester | 28 August 2013, 17:03:45 UTC | Updated `gmt` tab completion. | 28 August 2013, 17:03:45 UTC |
f088c59 | APipe Tester | 28 August 2013, 17:02:46 UTC | Updated `genome` tab completion. | 28 August 2013, 17:02:46 UTC |
4f21616 | APipe Tester | 28 August 2013, 17:00:25 UTC | Updated class browser cache. | 28 August 2013, 17:00:25 UTC |
b49682e | Chris Miller | 28 August 2013, 16:15:50 UTC | added option to plot whole chromosomes | 28 August 2013, 16:19:06 UTC |
8d1821e | Eddie Belter | 28 August 2013, 16:10:56 UTC | Sync UAC: update status msgs | 28 August 2013, 16:11:16 UTC |
c8222f0 | Eddie Belter | 28 August 2013, 16:06:42 UTC | Sync UAC: update sql in genome project parts | 28 August 2013, 16:11:16 UTC |
936835b | Dave Larson | 28 August 2013, 15:41:35 UTC | fix missing semicolon error | 28 August 2013, 15:41:35 UTC |
2a3e33d | Dave Larson | 21 August 2013, 16:08:22 UTC | forgot the FT filter tag in the header. doh! | 28 August 2013, 15:38:50 UTC |
50fc9db | Dave Larson | 21 August 2013, 11:08:56 UTC | add FT field for better merging | 28 August 2013, 15:38:49 UTC |
f58f64d | Dave Larson | 21 August 2013, 10:52:49 UTC | add the ability to skip header lines during the sort | 28 August 2013, 15:38:49 UTC |
60179b1 | Dave Larson | 21 August 2013, 10:50:49 UTC | set aligned_reads_sample name | 28 August 2013, 15:38:48 UTC |
f7b80f4 | Dave Larson | 21 August 2013, 04:25:58 UTC | fix some file naming and take advantage of new line skipping functionality in the sort | 28 August 2013, 15:38:48 UTC |
5ff5305 | Dave Larson | 21 August 2013, 01:56:41 UTC | handle the case where depth is 0 in the FA contamination | 28 August 2013, 15:38:47 UTC |
1336329 | Adam Coffman | 28 August 2013, 15:04:41 UTC | sort on date rather than id | 28 August 2013, 15:04:41 UTC |
1700d13 | Thomas Mooney | 28 August 2013, 14:06:15 UTC | Lowercase the column names now that we're on PG. This clears up errors like: While committing, metadata for table input does not match class Genome::SoftwareResult::Input::Ghost. Table primary key columns are software_result_id, input_name class ID property columns software_result_id, INPUT_NAME | 28 August 2013, 14:06:15 UTC |
70037a4 | APipe Tester | 28 August 2013, 01:59:29 UTC | Updated `genome` tab completion. | 28 August 2013, 01:59:29 UTC |
2a7e5cf | APipe Tester | 28 August 2013, 01:57:25 UTC | Updated class browser cache. | 28 August 2013, 01:57:25 UTC |
2ffc52f | Travis Abbott | 28 August 2013, 01:28:42 UTC | fix typo: disk_allocation => disk_allocations. | 28 August 2013, 01:28:42 UTC |
24bd0ba | Obi Griffith | 28 August 2013, 00:26:49 UTC | blessed clinseq diffs related to limfo output | 28 August 2013, 00:26:49 UTC |
35fe10b | Eddie Belter | 27 August 2013, 21:13:19 UTC | Sync UAC: do not order by id | 27 August 2013, 21:18:41 UTC |
712226d | Eddie Belter | 27 August 2013, 21:12:21 UTC | Sync Expunge: do not delete [temporary] | 27 August 2013, 21:18:40 UTC |
5cdef50 | Eddie Belter | 27 August 2013, 21:11:53 UTC | Sync UAC: cleanup - rm test stuff and unused methods | 27 August 2013, 21:18:40 UTC |
70cc531 | Eddie Belter | 27 August 2013, 20:28:29 UTC | Sync UAC: calculate and add missing to report | 27 August 2013, 21:18:39 UTC |
2f4c2c3 | Eddie Belter | 27 August 2013, 20:20:17 UTC | Sync UAC: method for creating genome objects | 27 August 2013, 21:18:39 UTC |
880a40a | Eddie Belter | 27 August 2013, 19:41:43 UTC | Sync UAC: rm sync order | 27 August 2013, 21:18:38 UTC |
9ca4fbf | Eddie Belter | 27 August 2013, 19:40:21 UTC | Sync UAC: add get ids for class; rm all unneeded execute block | 27 August 2013, 21:18:38 UTC |
aab72f2 | Eddie Belter | 27 August 2013, 19:20:53 UTC | Sync UAC: extract locking into separate methods | 27 August 2013, 21:18:37 UTC |
088a1a2 | Anthony Brummett | 27 August 2013, 21:08:46 UTC | typo | 27 August 2013, 21:08:46 UTC |
5e26e7d | Nathan Nutter | 27 August 2013, 20:50:33 UTC | IDs are Text now so have to be quoted in JSON... in XSL... in XML... | 27 August 2013, 20:50:55 UTC |
d88a845 | APipe Tester | 27 August 2013, 20:46:48 UTC | Updated `genome` tab completion. | 27 August 2013, 20:46:48 UTC |
3a80cb7 | APipe Tester | 27 August 2013, 20:44:54 UTC | Updated class browser cache. | 27 August 2013, 20:44:54 UTC |
9cc0d97 | Anthony Brummett | 27 August 2013, 20:34:16 UTC | Instead of picking the "latest" library, exit when there are more than one with the given name As part of the postgres-id-sorting change, we can't rely on the "highest" ID being the newest thing anymore. There's no obvious time associated with a library so no good way to keep the old behavior, which seems bad anyway | 27 August 2013, 20:34:16 UTC |
8cd41b3 | Anthony Brummett | 27 August 2013, 20:33:54 UTC | Can't sort numerically be ID anymore | 27 August 2013, 20:33:54 UTC |
f3bd359 | Anthony Brummett | 27 August 2013, 20:33:13 UTC | Can't sort things by ID as a surrogate for sorting by creation order | 27 August 2013, 20:33:13 UTC |
841cbb1 | Adam Coffman | 27 August 2013, 19:58:47 UTC | remove unused sub | 27 August 2013, 19:58:47 UTC |
3a7faf9 | Adam Coffman | 27 August 2013, 19:58:28 UTC | compare ids as strings instead of numbers | 27 August 2013, 19:58:28 UTC |
52f1a4e | Adam Coffman | 27 August 2013, 19:57:48 UTC | sort ids as strings instead of numbers | 27 August 2013, 19:57:48 UTC |
51bade9 | Adam Coffman | 27 August 2013, 19:57:28 UTC | sort on date_scheduled instead of build id | 27 August 2013, 19:57:28 UTC |
9ceb84e | Adam Coffman | 27 August 2013, 19:56:34 UTC | use last_succeeded_build | 27 August 2013, 19:56:34 UTC |
c9de8fb | Adam Coffman | 27 August 2013, 19:55:43 UTC | sort bamqc result by new best_guess_date value on software results | 27 August 2013, 19:55:43 UTC |
48f6172 | Adam Coffman | 27 August 2013, 19:54:25 UTC | sort on creation_date and date_scheduled instead of id | 27 August 2013, 19:54:25 UTC |
cf30083 | Adam Coffman | 27 August 2013, 19:54:02 UTC | sort instrument data ids as strings | 27 August 2013, 19:54:02 UTC |
730ae22 | Adam Coffman | 27 August 2013, 19:53:15 UTC | sort models on creation date instead of id | 27 August 2013, 19:53:15 UTC |
2478e2e | Adam Coffman | 27 August 2013, 19:52:24 UTC | sort models on creation date instead of id | 27 August 2013, 19:52:24 UTC |
10a5c10 | Adam Coffman | 27 August 2013, 19:51:57 UTC | sort instrument data ids as strings | 27 August 2013, 19:51:57 UTC |
9e4b959 | Adam Coffman | 27 August 2013, 19:51:35 UTC | sort build ids as strings instead of numbers | 27 August 2013, 19:51:35 UTC |
3e5f6ef | Adam Coffman | 27 August 2013, 19:51:18 UTC | sort builds on date_scheduled instead of id | 27 August 2013, 19:51:18 UTC |
647e572 | Adam Coffman | 27 August 2013, 19:42:00 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 27 August 2013, 19:42:00 UTC |
0fd5d84 | Adam Coffman | 27 August 2013, 19:41:49 UTC | add new best_guess_date sub for sorting software result | 27 August 2013, 19:41:49 UTC |
57ea583 | APipe Tester | 27 August 2013, 19:31:54 UTC | updated ur submodule to e3864f9 | 27 August 2013, 19:31:54 UTC |
5d5987f | APipe Tester | 27 August 2013, 19:24:34 UTC | updated graphite submodule to da9443f | 27 August 2013, 19:24:34 UTC |
255d147 | Nathan Nutter | 27 August 2013, 18:41:30 UTC | remove old datasources | 27 August 2013, 18:41:30 UTC |
b99328f | Travis Abbott | 27 August 2013, 18:33:19 UTC | update model set coverage view to find correct builds it previously tried to sort builds by id, but build ids are no longer numeric. now, $model->builds returns builds newest first, which is what this thing wants anyway. | 27 August 2013, 18:34:33 UTC |
f77e912 | Travis Abbott | 27 August 2013, 17:43:38 UTC | Genome::Model->builds now returns builds in order (newest first) they are ordered by date_scheduled (descending) | 27 August 2013, 18:34:33 UTC |
078c0df | APipe Tester | 27 August 2013, 18:17:56 UTC | updated graphite submodule to f4151f8 | 27 August 2013, 18:17:56 UTC |
02423fb | Gabriel Sanderson | 27 August 2013, 17:57:21 UTC | Merge branch 'master' into gb_master | 27 August 2013, 17:57:21 UTC |
a88ea93 | Gabriel Sanderson | 27 August 2013, 17:56:26 UTC | Add a VERY rudimentary check to the beginning that will look for the common problem that we have "chr" chromosomes without a nimblegen reference sequence. | 27 August 2013, 17:56:26 UTC |
1eb3b61 | APipe Tester | 27 August 2013, 15:47:05 UTC | updated graphite submodule to 1629c7e | 27 August 2013, 15:47:05 UTC |
05b227e | Mark Burnett | 27 August 2013, 15:37:38 UTC | G:D:Allocation test -- seed RNG on fork This should fix the bug related to my previous commit. | 27 August 2013, 15:37:38 UTC |
d98687b | Mark Burnett | 27 August 2013, 15:30:16 UTC | change G:D:A test allocation_paths This is an attempt to fix this error: ERROR: Failed to create directory (/tmp/allocation_testing_2v2Wmv/test_volume_2_hibzxi6/testing//tmp/allocation_testing_2v2Wmv/test_volume_2_hibzxi6/allocation_lock_testing_1_pKhDg6d) with return value = '', and error: Can't mkdir('/tmp/allocation_testing_2v2Wmv/test_volume_2_hibzxi6/testing'): File exists at /gscmnt/gc13001/info/model_data/apipe-ci/workspace/1-Genome-Perl-Tests/PERL_VERSION=5.10/PERL_VERSION/5.10/lib/perl/Genome/Sys.pm line 839 ERROR: Can't mkdir('/tmp/allocation_testing_2v2Wmv/test_volume_2_hibzxi6/testing'): File exists at /gscmnt/gc13001/info/model_data/apipe-ci/workspace/1-Genome-Perl-Tests/PERL_VERSION=5.10/PERL_VERSION/5.10/lib/perl/Genome/Sys.pm line 839 I could not reproduce the error, but this change should fix the odd, nested path. | 27 August 2013, 15:32:18 UTC |
4c1b012 | Thomas Mooney | 27 August 2013, 15:23:44 UTC | Take fail count into consideration when deciding which data to process. | 27 August 2013, 15:23:44 UTC |
1e078c6 | Mark Burnett | 27 August 2013, 13:33:39 UTC | G:M:T:Picard monitors both stdout and stderr for activity | 27 August 2013, 14:09:50 UTC |
cf50bfc | Mark Burnett | 27 August 2013, 13:32:55 UTC | make sure InstrumentData::delete removes BamQc results | 27 August 2013, 14:09:49 UTC |
c0325c1 | Mark Burnett | 23 August 2013, 14:56:16 UTC | add note indicating a build is run using flow | 27 August 2013, 14:09:49 UTC |
61bcd43 | Thomas Mooney | 27 August 2013, 14:05:30 UTC | Updates to account for transition to UUIDs. | 27 August 2013, 14:05:30 UTC |
29bd72e | Thomas Mooney | 27 August 2013, 13:49:27 UTC | Improve error message--print just class name instead of metaobject hash. | 27 August 2013, 13:49:27 UTC |
9cda567 | APipe Tester | 26 August 2013, 23:22:02 UTC | updated workflow submodule to f9affd1 | 26 August 2013, 23:22:02 UTC |
62ea041 | Feiyu Du | 26 August 2013, 22:22:39 UTC | add output default to STDOUT | 26 August 2013, 22:22:39 UTC |
8b473d9 | APipe Tester | 26 August 2013, 20:48:40 UTC | Updated `gmt` tab completion. | 26 August 2013, 20:48:40 UTC |
9dfa0d2 | APipe Tester | 26 August 2013, 20:47:39 UTC | Updated `genome` tab completion. | 26 August 2013, 20:47:39 UTC |
050a1f8 | APipe Tester | 26 August 2013, 20:45:49 UTC | Updated class browser cache. | 26 August 2013, 20:45:49 UTC |
18f5021 | Dan Koboldt | 26 August 2013, 20:21:36 UTC | Writing something here. Merge branch 'master' of git+ssh://git/srv/git/genome | 26 August 2013, 20:21:36 UTC |
f85d020 | APipe Tester | 26 August 2013, 20:19:12 UTC | Updated `gmt` tab completion. | 26 August 2013, 20:19:12 UTC |
0af579a | APipe Tester | 26 August 2013, 20:18:06 UTC | Updated `genome` tab completion. | 26 August 2013, 20:18:06 UTC |
d8af0fa | APipe Tester | 26 August 2013, 20:15:43 UTC | Updated class browser cache. | 26 August 2013, 20:15:43 UTC |
06a4444 | Dan Koboldt | 26 August 2013, 20:11:12 UTC | Updates to Mendelian analysis tools | 26 August 2013, 20:11:12 UTC |
3f18253 | Nathan Nutter | 26 August 2013, 19:26:48 UTC | Merge Postgres transition branch | 26 August 2013, 19:26:48 UTC |
810d6bf | Nathan Nutter | 23 August 2013, 20:26:50 UTC | remove Genome::DataSource::Main | 26 August 2013, 19:18:30 UTC |
3134ae7 | Nathan Nutter | 23 August 2013, 20:26:41 UTC | remove use of Genome::DataSource::Main | 26 August 2013, 19:18:30 UTC |
ef4bca8 | Nathan Nutter | 23 August 2013, 19:00:09 UTC | remove Genome::DataSource::PGTest | 26 August 2013, 19:18:29 UTC |
f36c89b | Nathan Nutter | 23 August 2013, 18:59:31 UTC | remove GENOME_QUERY_POSTGRES | 26 August 2013, 19:18:29 UTC |
32a3b9c | Nathan Nutter | 23 August 2013, 18:59:10 UTC | remove use of GENOME_QUERY_POSTGRES | 26 August 2013, 19:18:28 UTC |
8b03865 | Anthony Brummett | 22 August 2013, 20:38:23 UTC | Data source pointed to the old Oracle schema The graphite metrics collector will use this to look up session info. We'd like to see the session count drop to 0 | 26 August 2013, 19:18:27 UTC |
d1227d1 | Anthony Brummett | 20 August 2013, 23:47:17 UTC | fix expected output wrt oracle date vs pg date format | 26 August 2013, 19:18:27 UTC |
ef4425e | Anthony Brummett | 20 August 2013, 23:28:40 UTC | Make Model/Command/Import/Metadata.t test pass This replays part of commit 89ebc0cbd7398ca5e8c31445e46ea6a8afc336de which was undone by commit 65e970fb2b36deef08d1773fafec1b419dd892eb | 26 August 2013, 19:18:26 UTC |
38a760e | Nathan Nutter | 13 August 2013, 20:08:38 UTC | add OldGMSchema | 26 August 2013, 19:18:26 UTC |
6a92d5a | Nathan Nutter | 02 August 2013, 03:46:40 UTC | update Meta DB for Postgres | 26 August 2013, 19:18:25 UTC |
dbd6ab0 | Ben Oberkfell | 30 July 2013, 23:43:02 UTC | columns are case sensitive | 26 August 2013, 19:18:24 UTC |
f1d449d | Ben Oberkfell | 30 July 2013, 17:15:07 UTC | fix expected output wrt oracle date vs pg date format | 26 August 2013, 19:18:24 UTC |
94f1bd9 | Nathan Nutter | 26 July 2013, 21:44:18 UTC | update channel_for_model to work with UUIDs | 26 August 2013, 19:18:23 UTC |
54cac01 | Nathan Nutter | 14 August 2013, 01:39:35 UTC | IDs are now 32 character text (UUID) | 26 August 2013, 19:18:23 UTC |
947fbc6 | Nathan Nutter | 15 August 2013, 17:37:24 UTC | all classes now use UUID generators | 26 August 2013, 19:18:21 UTC |
69525a8 | Nathan Nutter | 15 August 2013, 17:36:19 UTC | update table_names to match Postgres schema | 26 August 2013, 19:18:21 UTC |
449cc3e | Nathan Nutter | 23 August 2013, 20:23:37 UTC | remove GMSchemaOracle | 26 August 2013, 19:18:20 UTC |
bf9bf19 | Ben Oberkfell | 11 July 2013, 21:39:16 UTC | switch GMSchema to Postgres | 26 August 2013, 19:18:19 UTC |