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https://github.com/genome/genome
23 March 2024, 19:04:16 UTC
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Revision Author Date Message Commit Date
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
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