08e710d | Nathan Nutter | 16 December 2013, 15:59:12 UTC | remove dependency on Git::Repository | 16 December 2013, 15:59:12 UTC |
3bf1414 | Avinash Ramu | 14 December 2013, 15:25:19 UTC | copy over unfiltered fusion, fix small error in copying annotated fusions | 14 December 2013, 15:25:36 UTC |
5fcb784 | APipe Tester | 14 December 2013, 13:17:07 UTC | Updated `gmt` tab completion. | 14 December 2013, 13:17:07 UTC |
2d07103 | APipe Tester | 14 December 2013, 13:16:22 UTC | Updated `genome` tab completion. | 14 December 2013, 13:16:22 UTC |
8e83b83 | Nathan Nutter | 13 December 2013, 21:51:08 UTC | mark many GENOME_* variables as required If we defined a value in Genome::Site::TGI and a default_value was not supplied then these are now "required" configuration. A few exceptions were: GENOME_DEV_MODE GENOME_STATSD_HOST GENOME_STATSD_PORT We can decide later whether not having these set should be a compile-time or run-time error. For now we have to be careful about failing when they are not set since the code that uses them is probably not very defensive about it. | 13 December 2013, 22:13:41 UTC |
7ff790b | Nathan Nutter | 13 December 2013, 21:37:51 UTC | add missing package declarations | 13 December 2013, 21:37:51 UTC |
249ce49 | Nathan Nutter | 13 December 2013, 20:11:18 UTC | inherit import from Genome::Env::Required Instead of using side effect of `use Genome::Env::Required` inherit the import method with the requirement check. | 13 December 2013, 20:11:18 UTC |
8c1f0dd | Nathan Nutter | 13 December 2013, 20:10:01 UTC | add NAME | 13 December 2013, 20:10:01 UTC |
6b0b5e2 | Nathan Nutter | 13 December 2013, 19:58:43 UTC | rename to make consistent with others | 13 December 2013, 19:58:43 UTC |
d5607a9 | Nathan Nutter | 13 December 2013, 19:49:46 UTC | remove Env tests since they don't define classes | 13 December 2013, 19:49:46 UTC |
8c93642 | Nathan Nutter | 13 December 2013, 19:03:39 UTC | add test to catch and case sensitive files | 13 December 2013, 19:03:54 UTC |
76c1d98 | Anthony Brummett | 13 December 2013, 17:20:13 UTC | Switch to using Genome::Utility::Email from MIME::Lite Also added function Genome::Utility::Email::construct_address() | 13 December 2013, 17:23:51 UTC |
289f600 | Anthony Brummett | 13 December 2013, 17:16:58 UTC | add configuration for the email domain name | 13 December 2013, 17:23:32 UTC |
2e07e44 | Anthony Brummett | 11 December 2013, 23:17:46 UTC | add configuration for the apipe mail alias | 13 December 2013, 17:23:26 UTC |
2abf7b1 | Anthony Brummett | 11 December 2013, 23:14:17 UTC | add configuration for the SMTP server name | 13 December 2013, 17:23:25 UTC |
302808f | Anthony Brummett | 11 December 2013, 23:03:01 UTC | add configuration for a test email address | 13 December 2013, 17:23:23 UTC |
6f4178a | Anthony Brummett | 11 December 2013, 22:47:16 UTC | add configuration for a "noisy" system generated mail address | 13 December 2013, 17:23:20 UTC |
22ef7e0 | Anthony Brummett | 11 December 2013, 22:44:35 UTC | add configuration for a "no reply" email address | 13 December 2013, 17:23:19 UTC |
3610867 | Anthony Brummett | 11 December 2013, 22:43:07 UTC | add configuration for illumina bwa report mail alias | 13 December 2013, 17:23:18 UTC |
27d86d1 | Anthony Brummett | 11 December 2013, 22:27:39 UTC | Add configuration for the virome screening email alias | 13 December 2013, 17:23:17 UTC |
4884daf | Anthony Brummett | 10 December 2013, 22:56:40 UTC | replace example email addresses with non-tgi addresses | 13 December 2013, 17:23:16 UTC |
c86eb5a | Anthony Brummett | 10 December 2013, 21:13:50 UTC | utility module to send email | 13 December 2013, 17:23:15 UTC |
8217929 | Anthony Brummett | 10 December 2013, 20:27:25 UTC | remove large commented-out section | 13 December 2013, 17:23:14 UTC |
978b9c6 | Anthony Brummett | 10 December 2013, 17:30:21 UTC | Add method to construct an owner_id from the USER and GENOME_EMAIL_DOMAIN env vars | 13 December 2013, 17:23:12 UTC |
04a6258 | Kyung Kim | 13 December 2013, 16:56:51 UTC | Added additional params | 13 December 2013, 16:56:51 UTC |
aaf5ca5 | Avinash Ramu | 13 December 2013, 15:44:11 UTC | updated arguments to Genome::Sys->copy(takes only files, not dirs as params). create fusion dir even if WGS build does not exist. | 13 December 2013, 15:45:52 UTC |
5435890 | APipe Tester | 13 December 2013, 13:17:20 UTC | Updated `gmt` tab completion. | 13 December 2013, 13:17:20 UTC |
b58e7cf | APipe Tester | 13 December 2013, 13:16:36 UTC | Updated `genome` tab completion. | 13 December 2013, 13:16:36 UTC |
656e09c | Obi Griffith | 13 December 2013, 00:23:57 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 13 December 2013, 00:23:57 UTC |
a93c6a0 | Obi Griffith | 13 December 2013, 00:23:29 UTC | updated usage and docs for CView | 13 December 2013, 00:23:29 UTC |
4621349 | Chris Miller | 12 December 2013, 23:56:01 UTC | igv reference shouldn't default to b36, should be required param | 12 December 2013, 23:56:33 UTC |
f1c8ea8 | Avinash Ramu | 12 December 2013, 23:46:21 UTC | copy over fusion files even when there are no SV files | 12 December 2013, 23:46:39 UTC |
8acd064 | Kyung Kim | 12 December 2013, 23:37:04 UTC | Added ability to use flexbar v230 which has different params than earlier versions | 12 December 2013, 23:37:04 UTC |
01f146f | Avinash Ramu | 12 December 2013, 23:29:19 UTC | update clinseq.pm to not do filtering(this is now done in the RNAseq pipeline), just do intersection of fusion calls with SVs | 12 December 2013, 23:29:48 UTC |
7538b60 | apregier | 12 December 2013, 20:08:11 UTC | Merge branch 'copy' into gb_master | 12 December 2013, 20:08:11 UTC |
12bc286 | apregier | 12 December 2013, 19:43:47 UTC | Must cbind before the order changes cbind assumes that the arrays will be in the same order, but topTags changes the order. cbind must happen first. | 12 December 2013, 20:05:54 UTC |
245b0ff | apregier | 11 December 2013, 21:09:57 UTC | Add sdrf file to idf output Set the sdrf file name on the idf object Add additional required IDF row headers | 12 December 2013, 20:05:53 UTC |
e0d8247 | Malachi Griffith | 12 December 2013, 17:43:24 UTC | ClinSeq: minor update to documentation | 12 December 2013, 17:43:24 UTC |
080e2ac | APipe Tester | 12 December 2013, 13:16:20 UTC | Updated `genome` tab completion. | 12 December 2013, 13:16:20 UTC |
470b464 | APipe Tester | 12 December 2013, 13:14:38 UTC | Updated class browser cache. | 12 December 2013, 13:14:38 UTC |
5b0f66c | Susanna Siebert | 09 December 2013, 14:32:02 UTC | removed debug breakpoint | 11 December 2013, 21:06:07 UTC |
4c8ce81 | Susanna Siebert | 06 December 2013, 22:48:36 UTC | added wrapper to run EdgeR for ClinSeq including making the gene counts file and filtering | 11 December 2013, 21:06:01 UTC |
8efdb73 | Susanna Siebert | 06 December 2013, 21:46:56 UTC | added filtering functionality for gene counts files | 11 December 2013, 21:05:51 UTC |
2692834 | Susanna Siebert | 06 December 2013, 20:51:15 UTC | Make parameter names more intuitive | 11 December 2013, 21:05:42 UTC |
86f27b5 | Susanna Siebert | 11 December 2013, 20:43:07 UTC | empty genotype file is not a failure just return early | 11 December 2013, 20:43:17 UTC |
b4a5a2a | Eddie Belter | 11 December 2013, 18:45:16 UTC | MC16s: get SX results ind for each instdata when merging | 11 December 2013, 18:45:16 UTC |
33919c0 | APipe Tester | 11 December 2013, 13:18:19 UTC | Updated `gmt` tab completion. | 11 December 2013, 13:18:19 UTC |
ea9d10e | APipe Tester | 11 December 2013, 13:17:36 UTC | Updated `genome` tab completion. | 11 December 2013, 13:17:36 UTC |
4e2fbd9 | APipe Tester | 11 December 2013, 13:16:05 UTC | Updated class browser cache. | 11 December 2013, 13:16:05 UTC |
d00cef8 | Mark Burnett | 10 December 2013, 21:47:32 UTC | add support for Converge to WorkflowBuilder | 10 December 2013, 21:48:37 UTC |
0f00623 | Mark Burnett | 10 December 2013, 20:42:57 UTC | move responsibility for sorting input/output properties This will allow us to add new operation types that depend on particular sort order for their inputs and outputs (like Converge). | 10 December 2013, 21:48:36 UTC |
893065b | Charles Lu | 10 December 2013, 21:46:01 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 10 December 2013, 21:46:01 UTC |
6210aef | Charles Lu | 10 December 2013, 21:45:54 UTC | make --bmr-output option not required | 10 December 2013, 21:45:54 UTC |
ec64e62 | Chris Miller | 10 December 2013, 20:18:56 UTC | adding a new tool that appends Exome Variant Server allele frequencies to an annotation file | 10 December 2013, 20:19:29 UTC |
602528d | Jim Weible | 10 December 2013, 15:56:38 UTC | update rna-seq expected docs for cancer-annotation-db | 10 December 2013, 15:56:38 UTC |
faa715f | Jim Weible | 10 December 2013, 15:42:26 UTC | update apipe-test-rnaseq to remove cancer-annotation-db from the processing profile | 10 December 2013, 15:42:41 UTC |
1ebbc19 | Jim Weible | 10 December 2013, 15:41:48 UTC | make cancer_annoation_db an input rather than a processing-profile param | 10 December 2013, 15:42:40 UTC |
efccfb1 | Jim Weible | 10 December 2013, 15:02:01 UTC | Revert "update apipe-test-rnaseq to have new processing profile param" This reverts commit e587bedc1c4e174e1b01077d6e889dd9219d1688. cancer_annotation_db should never have been a processing profile param. It should be an input | 10 December 2013, 15:42:40 UTC |
8cb51ed | APipe Tester | 10 December 2013, 14:43:18 UTC | updated jenkins submodule to 73300ad | 10 December 2013, 14:43:18 UTC |
7dc8847 | APipe Tester | 10 December 2013, 13:17:26 UTC | Updated `genome` tab completion. | 10 December 2013, 13:17:26 UTC |
42e8ea7 | APipe Tester | 10 December 2013, 13:15:53 UTC | Updated class browser cache. | 10 December 2013, 13:15:53 UTC |
a521712 | Thomas Mooney | 09 December 2013, 23:33:43 UTC | Sort in the order we expect them to be sorted in. Same fix as 83ef80b86d83a1707040d22b1c276c9fdfd2f4d3. | 09 December 2013, 23:33:43 UTC |
0454870 | Adam Coffman | 09 December 2013, 22:45:33 UTC | dont resuse config hash references | 09 December 2013, 22:45:33 UTC |
d8981b5 | Thomas Mooney | 09 December 2013, 20:20:29 UTC | Fallback on any available GTF file for the annotation build. | 09 December 2013, 21:05:06 UTC |
a1da992 | Feiyu Du | 09 December 2013, 20:59:34 UTC | add solution for another case of indelfilter normal genotype | 09 December 2013, 20:59:34 UTC |
bfa13b1 | Adam Coffman | 09 December 2013, 18:41:40 UTC | update analysis project lister | 09 December 2013, 18:41:40 UTC |
cf12f8b | Adam Coffman | 09 December 2013, 17:00:01 UTC | small CQID fixes | 09 December 2013, 17:00:01 UTC |
83ef80b | Susanna Siebert | 09 December 2013, 16:29:25 UTC | sort instrument data by read group instead of date | 09 December 2013, 16:29:25 UTC |
e587bed | Jim Weible | 09 December 2013, 15:07:45 UTC | update apipe-test-rnaseq to have new processing profile param | 09 December 2013, 15:08:14 UTC |
8b10e7b | Jim Weible | 06 December 2013, 19:49:53 UTC | add Annotation to RnaSeq fusion detection | 09 December 2013, 15:08:13 UTC |
64117b2 | APipe Tester | 07 December 2013, 13:17:07 UTC | Updated `genome` tab completion. | 07 December 2013, 13:17:07 UTC |
c331c02 | APipe Tester | 07 December 2013, 13:15:30 UTC | Updated class browser cache. | 07 December 2013, 13:15:30 UTC |
d18093b | apregier | 06 December 2013, 22:31:12 UTC | Merge branch 'copy' into gb_master | 06 December 2013, 22:31:12 UTC |
7c7abe8 | apregier | 06 December 2013, 22:29:51 UTC | Use topTags to get adjusted p-value | 06 December 2013, 22:30:56 UTC |
995c846 | apregier | 06 December 2013, 22:11:16 UTC | Use topTags to get adjusted p-value | 06 December 2013, 22:30:55 UTC |
60b967f | Anthony Brummett | 06 December 2013, 21:20:55 UTC | tag the sqitch schema as synced with production | 06 December 2013, 21:36:13 UTC |
6e7f5ae | Anthony Brummett | 04 December 2013, 22:18:39 UTC | rename indexes to match the production database | 06 December 2013, 21:36:12 UTC |
0a331d7 | Anthony Brummett | 04 December 2013, 21:33:24 UTC | rename index to match what is in production DB | 06 December 2013, 21:36:12 UTC |
29ee6be | Anthony Brummett | 04 December 2013, 21:12:33 UTC | set permissions on config.instrument_data_analysis_project_bridge | 06 December 2013, 21:36:11 UTC |
c472f04 | Anthony Brummett | 04 December 2013, 21:01:48 UTC | change the name of the index to match what is in the production DB | 06 December 2013, 21:36:10 UTC |
7625257 | Anthony Brummett | 04 December 2013, 20:53:49 UTC | drop column disk.preserved and add NOT NULL to archive_after_time and status | 06 December 2013, 21:36:09 UTC |
24bcedc | apregier | 06 December 2013, 21:14:39 UTC | Merge branch 'copy' into gb_master | 06 December 2013, 21:14:39 UTC |
02157e4 | apregier | 06 December 2013, 21:12:48 UTC | Add header to counts_file | 06 December 2013, 21:12:48 UTC |
e88cb6d | apregier | 06 December 2013, 20:34:33 UTC | Don't explicitly set groups in DGEList object | 06 December 2013, 20:34:33 UTC |
90031cc | Susanna Siebert | 06 December 2013, 17:14:01 UTC | Replaced the rnaseq tumor and normal parameters with clinseq parameter | 06 December 2013, 20:16:23 UTC |
73f5ee2 | Susanna Siebert | 06 December 2013, 15:27:41 UTC | subjects_list and groups_list are optional parameters | 06 December 2013, 20:16:23 UTC |
4a506fa | Susanna Siebert | 05 December 2013, 22:36:28 UTC | Added test to ensure that the gene columns of the input files are identical | 06 December 2013, 20:16:22 UTC |
d421890 | Susanna Siebert | 05 December 2013, 22:30:33 UTC | Added test to ensure that the joined output file is as expected | 06 December 2013, 20:16:21 UTC |
c2b7cd1 | Susanna Siebert | 05 December 2013, 21:50:51 UTC | added new module to make a joined gene counts file for multiple RnaSeq builds | 06 December 2013, 20:16:21 UTC |
b405955 | Susanna Siebert | 04 December 2013, 17:57:02 UTC | Added validation and test to ensure that each subject is in each group at least once | 06 December 2013, 20:16:20 UTC |
3a1abe0 | Susanna Siebert | 04 December 2013, 17:36:47 UTC | Added validation and test to ensure that number of groups and subjects are the same | 06 December 2013, 20:16:20 UTC |
c7c7266 | Susanna Siebert | 04 December 2013, 17:28:18 UTC | Added validation and test to ensure that more than one subject is being used | 06 December 2013, 20:16:19 UTC |
783d23e | Susanna Siebert | 04 December 2013, 17:25:50 UTC | Added validation and test to ensure that each subject is being used more than once | 06 December 2013, 20:16:19 UTC |
e506ee9 | Susanna Siebert | 04 December 2013, 17:12:53 UTC | Added validation and test for having more than one group | 06 December 2013, 20:16:18 UTC |
e39bc2f | Susanna Siebert | 04 December 2013, 17:00:30 UTC | Factored out the validate params tests into Base.t | 06 December 2013, 20:16:17 UTC |
31fc275 | Susanna Siebert | 04 December 2013, 16:49:57 UTC | updated the documentation for the GLM module | 06 December 2013, 20:16:17 UTC |
6056ea0 | Susanna Siebert | 04 December 2013, 16:48:23 UTC | refactored the parameter validation | 06 December 2013, 20:16:16 UTC |
d8d8140 | Susanna Siebert | 03 December 2013, 22:41:27 UTC | added edgeR GLM functionality and tests | 06 December 2013, 20:16:16 UTC |
e08309c | Susanna Siebert | 03 December 2013, 22:40:33 UTC | factored out the generate_counts_file subroutine into the base class so it can be used by both tests for classic and glm | 06 December 2013, 20:16:15 UTC |
b6f9ab4 | Susanna Siebert | 03 December 2013, 21:30:28 UTC | updated documentation to correspond to edgeR's updated output file header names | 06 December 2013, 20:16:15 UTC |