Skip to main content

Browse the archive

https://github.com/genome/genome
23 March 2024, 19:04:16 UTC
sort by:
Revision Author Date Message Commit Date
312a299 apregier 18 April 2013, 04:14:21 UTC Bug fix 18 April 2013, 04:14:50 UTC
71f56cb Travis Abbott 17 April 2013, 21:44:41 UTC update clinseq test data to fix broken test 17 April 2013, 21:44:41 UTC
1d27bde Eddie Belter 17 April 2013, 19:26:01 UTC ClinSeq: update output for new builds 17 April 2013, 20:08:25 UTC
43cc8c3 Ian Ferguson 17 April 2013, 19:27:18 UTC Added 1; to end of some aligner modules 17 April 2013, 19:27:18 UTC
04cf5df Ian Ferguson 17 April 2013, 19:24:25 UTC Initial commit for Bwamem aligner module 17 April 2013, 19:24:25 UTC
107e345 Ian Ferguson 17 April 2013, 19:15:00 UTC Refactoring in GMT::Bwa Tried to refactor GMT::Bwa to better manage the many different versions and features of Bwa. Includes tests. 17 April 2013, 19:15:00 UTC
5195186 Adam Coffman 17 April 2013, 17:42:05 UTC add database entities to support analysis project configuration 17 April 2013, 17:42:05 UTC
1220f64 apregier 17 April 2013, 14:31:46 UTC Fix bug 17 April 2013, 14:31:46 UTC
027df79 apregier 16 April 2013, 22:33:24 UTC Remove hard-coded path to sv annotation files 16 April 2013, 22:48:27 UTC
d564199 Eddie Belter 16 April 2013, 22:45:51 UTC Sync: fix recocile test 16 April 2013, 22:45:51 UTC
fc25052 Adam Coffman 16 April 2013, 21:55:21 UTC add new genome env variable to point to default analysis config location 16 April 2013, 21:55:21 UTC
3654a54 Eddie Belter 16 April 2013, 21:10:33 UTC Sync: _create_librarysummary points to _create_object 16 April 2013, 21:10:41 UTC
6867b57 Eddie Belter 16 April 2013, 21:09:15 UTC Sync: update apipe classes uses org sample in classes dir 16 April 2013, 21:10:40 UTC
65a9c4d Eddie Belter 16 April 2013, 18:19:32 UTC Sync: fix misc update test after removing is_control 16 April 2013, 21:10:40 UTC
c1a6499 Eddie Belter 16 April 2013, 17:58:09 UTC Sync: remove is_control from being synced 16 April 2013, 21:10:39 UTC
89ec1b0 Eddie Belter 16 April 2013, 17:57:32 UTC Sync: change smaple class used to organism sample in classes dir 16 April 2013, 21:10:39 UTC
a267888 Eddie Belter 16 April 2013, 16:46:16 UTC Sync: mv sample to organism sample 16 April 2013, 21:10:39 UTC
29b5f72 apregier 16 April 2013, 20:15:24 UTC Merge branch 'fix' into gb_master 16 April 2013, 20:15:24 UTC
5fe91ea apregier 11 April 2013, 21:52:12 UTC Add ensembl stable gene id column to transcript output Bug fix Update blessed builds 16 April 2013, 20:13:50 UTC
4cbd2a0 apregier 11 April 2013, 21:18:12 UTC Add unit test 16 April 2013, 20:13:46 UTC
fe7818b apregier 11 April 2013, 21:10:37 UTC Add unit test for segdup 16 April 2013, 20:13:45 UTC
5c36b1a apregier 03 April 2013, 20:04:19 UTC Improve sv annotation algorithm for dbsnp/dbvar/segdup Add unit tests Refactor to use interval tree -Add Set::IntervalTree package -genome-snapshot-deps Update blessed build 16 April 2013, 20:13:44 UTC
8bd427e APipe Tester 16 April 2013, 18:37:45 UTC updated jenkins submodule to cf04f73 16 April 2013, 18:37:45 UTC
ce74916 Adam Coffman 16 April 2013, 18:01:32 UTC add postgres mappings for new genome tables 16 April 2013, 18:01:32 UTC
95529e7 Mark Burnett 16 April 2013, 14:34:18 UTC add variants/*.{err,out} to ignored files (RefAlign & SomVar) 16 April 2013, 17:04:49 UTC
97f282e APipe Tester 16 April 2013, 16:02:41 UTC updated jenkins submodule to 7a9a1e4 16 April 2013, 16:02:41 UTC
00d156a Adam Coffman 16 April 2013, 14:41:34 UTC Add ObjectWithTimestamps mixin 16 April 2013, 14:41:34 UTC
ec340c7 Thomas Mooney 16 April 2013, 14:18:19 UTC Cleanup these temp files we're throwing around. 16 April 2013, 14:19:06 UTC
7e6e13f Ian Ferguson 15 April 2013, 19:12:41 UTC Restore GMT/Predictor/FastaChunker.pm FastaChunker was removed while cleaning up default parameters. Added it back to fix failing protein annotation builds. 15 April 2013, 19:12:41 UTC
5bad97c APipe Tester 15 April 2013, 15:39:15 UTC updated jenkins submodule to 19d09e5 15 April 2013, 15:39:15 UTC
172bc59 Thomas Mooney 15 April 2013, 15:33:20 UTC Only pull back results matching our test name. If a test name was added to some VCF results for our result after-the-fact, they would've been grabbed by this query even though the present build did not use them. 15 April 2013, 15:33:20 UTC
d2ef5b6 nnutter 15 April 2013, 13:49:26 UTC redirect stderr This was producing a *ton* of output in it's test so I opted to log stderr. If that is not an OK solution in general we'll still have to address the test. 15 April 2013, 13:49:26 UTC
5ce1ddc nnutter 15 April 2013, 13:49:08 UTC specify output_directories 15 April 2013, 13:49:08 UTC
3beb52a nnutter 15 April 2013, 13:29:15 UTC re-enable test Upstream builds finished building so re-enabled test. Add an additional test because it now get's the model's latest build instead of a specific build. Updated expected output which was mostly due to changes in build IDs and paths but there were also a few changes in output that looked minor. 15 April 2013, 13:30:41 UTC
f823d8e nnutter 15 April 2013, 13:28:34 UTC update expected output genome-model-rnaseq-list2.out has a new build. 15 April 2013, 13:28:34 UTC
507de3e APipe Tester 12 April 2013, 23:51:54 UTC updated graphite submodule to 466bfdb 12 April 2013, 23:51:54 UTC
7cfe2ab APipe Tester 12 April 2013, 23:51:47 UTC updated ur submodule to 334ab66 12 April 2013, 23:51:47 UTC
e1b8cb3 Adam Coffman 12 April 2013, 22:45:02 UTC Merge branch 'master' of ssh://git/srv/git/genome 12 April 2013, 22:45:02 UTC
ac0fd42 Adam Coffman 12 April 2013, 22:44:52 UTC create abstract parent classes for interfaces to use in configuration readers 12 April 2013, 22:44:52 UTC
66233b5 APipe Tester 12 April 2013, 21:46:17 UTC updated ur submodule to fb1b003 12 April 2013, 21:46:17 UTC
c5fca6f nnutter 12 April 2013, 21:33:49 UTC move _sync_database shortcut closer to source of problem This @changed_objects "shortcut" is to avoid an issue with autocommit on the Pg driver where it would cause an unwanted lock. This was previously in Command::Dispatch::Shell from UR commit 7fd973b. 12 April 2013, 21:35:48 UTC
90ba06d Adam Coffman 12 April 2013, 20:48:59 UTC add MaskedConfigurationReader to use in Analysis configuration 12 April 2013, 20:48:59 UTC
2e1c63c nnutter 12 April 2013, 19:33:14 UTC remove _lock_model_for_start It doesn't do anything to prevent duplicate builds but does cause intermittent failures when trying to start test models under different configurations. 12 April 2013, 20:11:53 UTC
8f9614f Adam Coffman 12 April 2013, 19:10:46 UTC remove breakpoint, whoops 12 April 2013, 19:10:46 UTC
737b7ce Adam Coffman 12 April 2013, 19:09:41 UTC add TreeCopy strategy for use in analysis configuration 12 April 2013, 19:09:41 UTC
51a9e6f nnutter 12 April 2013, 15:44:48 UTC Merge branch 'heartbeat' 12 April 2013, 18:17:41 UTC
eaa51a0 nnutter 12 April 2013, 15:43:11 UTC set "RnaSeq Alignment" to allow 7 days for max_elapsed_log_time 12 April 2013, 18:17:40 UTC
740f8a4 nnutter 12 April 2013, 15:35:05 UTC allow commands to specify the max_elapsed_log_time 12 April 2013, 18:17:38 UTC
20fd3b0 nnutter 12 April 2013, 15:34:37 UTC get logs from workflow instead of parsing bjobs 12 April 2013, 18:17:37 UTC
061077b Charles Lu 12 April 2013, 17:51:48 UTC Merge branch 'master' of ssh://git/srv/git/genome 12 April 2013, 17:51:48 UTC
21afb2f Charles Lu 12 April 2013, 17:51:42 UTC made --referene option required now 12 April 2013, 17:51:42 UTC
14651ab Gabriel Sanderson 12 April 2013, 17:34:19 UTC Merge branch 'master' into gb_master 12 April 2013, 17:34:19 UTC
3145890 Gabriel Sanderson 12 April 2013, 17:33:46 UTC Slightly clearer error when versions are a problem 12 April 2013, 17:33:55 UTC
76479bd Feiyu Du 12 April 2013, 15:45:07 UTC 1.add condition of empty contig.fasta for som-val pipeline; 2. bug fix for samtools mpileup snv vcf converter 12 April 2013, 15:45:07 UTC
5a9ba0e Adam Coffman 12 April 2013, 15:37:03 UTC add YAML parser to use in analysis project config 12 April 2013, 15:37:03 UTC
fe5acf2 APipe Tester 12 April 2013, 15:06:19 UTC Updated `gmt` tab completion. 12 April 2013, 15:06:19 UTC
89e07a4 APipe Tester 12 April 2013, 15:05:29 UTC Updated `genome` tab completion. 12 April 2013, 15:05:29 UTC
2a89318 APipe Tester 12 April 2013, 14:58:40 UTC Updated `genome` tab completion. 12 April 2013, 14:59:48 UTC
129c3e8 Adam Coffman 12 April 2013, 14:49:41 UTC Merge branch 'master' of ssh://git/srv/git/genome 12 April 2013, 14:49:41 UTC
d8e33af Adam Coffman 11 April 2013, 22:07:39 UTC Add tree handler class for use in analysis project config 12 April 2013, 14:48:46 UTC
cb9f82a nnutter 11 April 2013, 19:11:51 UTC approved new build after reviewing with Malachi There were several causes of changes: - Some files were added in: 9bb4d83 ClinSeq - generate clonality plots test now takes ~60s instead of ~1400s to run, other minor fixes - Some paths change due to rebuild of upstream models, e.g. tumor_rnaseq_build - Some floating point changes/error that correlated very strongly with previous. - Several log files were removed and are now inline. 11 April 2013, 19:15:09 UTC
8d2d644 Malachi Griffith 11 April 2013, 19:12:46 UTC Ignore .R.stderr files in build diffing 11 April 2013, 19:12:46 UTC
6462e53 Ben Oberkfell 11 April 2013, 16:51:50 UTC account for extra newline added so as to not break TAP 11 April 2013, 16:51:50 UTC
439cd64 nnutter 11 April 2013, 16:22:01 UTC update config for new home dirs 11 April 2013, 16:22:35 UTC
a46d069 nnutter 11 April 2013, 16:03:11 UTC add a new line so that bad programs don't break TAP, etc. 11 April 2013, 16:04:42 UTC
5c67dce nnutter 11 April 2013, 14:57:13 UTC example values were added in 6af42ec 11 April 2013, 14:57:13 UTC
b4a1731 nnutter 11 April 2013, 14:35:48 UTC Vep.d moved 11 April 2013, 14:35:48 UTC
5b529a2 nnutter 11 April 2013, 14:30:14 UTC new build looks OK to me It looks like a new alignment was done that had a few insignificant changes in the results. 11 April 2013, 14:30:14 UTC
9b2f47b nnutter 11 April 2013, 14:13:16 UTC blacklist all Db/Ensembl/Vep.d from being compile tested 11 April 2013, 14:13:51 UTC
6af42ec Scott Smith 11 April 2013, 13:42:28 UTC Restructure Genome/Db tree. 11 April 2013, 13:42:28 UTC
f92de5e nnutter 11 April 2013, 02:30:52 UTC revert default => example_values change This probably needs to be backfilled on SomaticValidation processing profiles and converted to an input to the model's workflow. 11 April 2013, 02:30:52 UTC
9d8d256 nnutter 11 April 2013, 02:15:57 UTC approved apipe-test-reference-alignment This model just started running with GENOME_SOFTWARE_RESULT_TEST_NAME so the alignments were regenerated for the first time in awhile. BWA alignments now use however many CPUs are available when submitted to LSF so the -t option changed to 4 and that was the only diff. diff -U0 <(samtools view -h /gscmnt/gc13001/info/model_data/2880887847/build133133153/alignments/112032366.bam) <(samtools view -h /gscmnt/gc9006/info/model_data/2880887847/build136534477/alignments/136537547.bam) --- /dev/fd/63 2013-04-10 21:12:53.057852876 -0500 +++ /dev/fd/62 2013-04-10 21:12:53.057852876 -0500 @@ -116 +116 @@ -@PG ID:2851949190 VN:0.5.9 CL:bwa aln -t4 -q 5; bwa sampe -a 462 +@PG ID:2851949190 VN:0.5.9 CL:bwa aln -t2 -q 5; bwa sampe -a 462 11 April 2013, 02:15:57 UTC
d5de8a0 nnutter 10 April 2013, 19:59:44 UTC updated expected outputs Updated `genome-model-rnaseq-list2.out` because a model has a new build. 10 April 2013, 19:59:44 UTC
96da6fa Gabriel Sanderson 10 April 2013, 19:24:48 UTC Merge branch 'master' into gb_master 10 April 2013, 19:24:48 UTC
baaa8e1 Gabriel Sanderson 10 April 2013, 19:23:54 UTC Increment vcf_version because old vcf results had no sample name set 10 April 2013, 19:24:04 UTC
293b831 Ben Oberkfell 10 April 2013, 18:57:45 UTC return to the previous behavior that didnt include the post-commit handler, while i figure out why it is janky 10 April 2013, 18:57:45 UTC
7b9f451 nnutter 10 April 2013, 03:19:02 UTC simplify 10 April 2013, 03:19:02 UTC
583a792 apregier 10 April 2013, 02:50:26 UTC Can't call object method before object is instantiated 10 April 2013, 02:50:26 UTC
451e577 nnutter 10 April 2013, 01:28:46 UTC rename function so it doesn't override instance method 10 April 2013, 01:31:29 UTC
14658a4 nnutter 09 April 2013, 20:54:37 UTC updated expected outputs Updated `genome-model-rnaseq-list2.out` because several models have had new builds. 09 April 2013, 20:54:37 UTC
0a74b16 Chris Miller 09 April 2013, 19:39:19 UTC create output dir if doesn't exist 09 April 2013, 19:41:11 UTC
54d29af nnutter 09 April 2013, 19:23:36 UTC add blacklist for exceptions 09 April 2013, 19:23:47 UTC
2d31a19 nnutter 09 April 2013, 19:23:22 UTC label test 09 April 2013, 19:23:46 UTC
e3c229a Jim Weible 08 April 2013, 18:59:33 UTC respect reference-fasta param for build purposes 09 April 2013, 19:18:21 UTC
651e1a9 Jim Weible 08 April 2013, 15:46:43 UTC MergeFile became MergeFiles and remove useless is_many 09 April 2013, 19:18:21 UTC
b5908f5 nnutter 09 April 2013, 19:11:09 UTC temporary bypass 09 April 2013, 19:11:09 UTC
a21b631 nnutter 09 April 2013, 19:05:09 UTC enable quiet option on VEP Enable quiet option so Bio::EnsEMBL::Variation::Utils::VEP doesn't spam logs with progress bar. 09 April 2013, 19:05:09 UTC
d500927 nnutter 09 April 2013, 18:56:29 UTC whitespace 09 April 2013, 18:56:29 UTC
a7b2dc0 nnutter 09 April 2013, 18:53:16 UTC limit output for test so it doesn't spam 09 April 2013, 18:54:34 UTC
3da234f APipe Tester 09 April 2013, 18:12:45 UTC updated jenkins submodule to 35ad2c1 09 April 2013, 18:12:45 UTC
d322d31 APipe Tester 09 April 2013, 17:59:07 UTC updated jenkins submodule to decd4bb 09 April 2013, 17:59:07 UTC
cb829ca Malachi Griffith 09 April 2013, 01:07:28 UTC Bringing R code used by ClonalityPlot.pm under source control 09 April 2013, 01:07:28 UTC
e994e16 Malachi Griffith 09 April 2013, 01:06:35 UTC ClonalityPlot.pm used to use a default path to some random R code on network that was then sourced, this was refactored to be specified as a required parameter. This broke a clin-seq command that wants to run this command automatically. I have refactored to bring the random code under source control and find it automatically instead of specifying at command line. 09 April 2013, 01:06:35 UTC
b5f1d8c Malachi Griffith 09 April 2013, 00:56:41 UTC ClinSeq - Added ad hoc ensembl API script to assist in creation of PCR primer design files 09 April 2013, 00:56:41 UTC
ea18fbe nnutter 08 April 2013, 23:57:47 UTC update expected output Updated `genome-model-rnaseq-list2.out` now that several builds have completed so several columns are now filled in with values instead of nulls. 08 April 2013, 23:57:47 UTC
9d03000 nnutter 08 April 2013, 22:47:58 UTC reapply most of Gabe's commit to remove default_values I mistakenly reverted a previous commit instead of only a couple files in it. This reapplies the rest of the changes. Erroneous Revert: 1da947a655ceb82bc450766333b21260ca20885d Original Change: 935b04397f9b925fac4b80aacbdcbcf79d70dea8 08 April 2013, 23:00:56 UTC
a210fc8 Eddie Belter 08 April 2013, 21:42:15 UTC InstData import: only dump primary alignemnts from sra 08 April 2013, 21:42:48 UTC
45bc9bd Eddie Belter 05 April 2013, 22:16:06 UTC InstData Import: check ncbi config file 08 April 2013, 21:42:48 UTC
cf348ec Eddie Belter 04 April 2013, 16:18:25 UTC InstData Import: Add SRA functionality 08 April 2013, 21:42:48 UTC
5d44179 Eddie Belter 01 April 2013, 18:40:36 UTC InstData Import: mv bam sort into separate method 08 April 2013, 21:42:47 UTC
back to top