| e08ab91 | Eddie Belter | 16 March 2015, 17:08:24 UTC | InstData Import: spelling and comment fixes | 16 March 2015, 17:08:24 UTC |
| 33c1a43 | Anthony Brummett | 16 March 2015, 14:41:53 UTC | Merge pull request #562 from brummett/error-message Avoid an additional error when we can't connect to the logging DB | 16 March 2015, 14:41:53 UTC |
| 9420883 | Anthony Brummett | 16 March 2015, 14:41:15 UTC | Merge pull request #561 from brummett/datetime Fix DateTime calculation involving DST | 16 March 2015, 14:41:15 UTC |
| 79ddb55 | Yevgeniy Gindin | 16 March 2015, 14:19:16 UTC | Made compatible with pysam version 0.7.8. | 16 March 2015, 14:19:16 UTC |
| 1b55686 | Susanna Siebert | 16 March 2015, 14:03:55 UTC | Merge pull request #563 from susannasiebert/picard_help_detail Fix help_detail links to point to correct anchor | 16 March 2015, 14:03:55 UTC |
| c9c90cb | Thomas B. Mooney | 16 March 2015, 13:47:55 UTC | Merge pull request #549 from tmooney/cqid_queries_undef_properties CQID: Only filter undef properties from model creation. | 16 March 2015, 13:47:55 UTC |
| 5cf6f2c | APipe Tester | 14 March 2015, 21:17:56 UTC | updated ur submodule to 7e7d60a | 14 March 2015, 21:17:56 UTC |
| a2a3da9 | Feiyu Du | 14 March 2015, 20:39:47 UTC | bugfix 1. make Htseq count to revivify the per lane bam from merged bam 2. input correct instrument_data_id to RecreatePerLaneBam | 14 March 2015, 20:39:47 UTC |
| f75c3f1 | APipe Tester | 14 March 2015, 00:27:39 UTC | updated jenkins submodule to e661237 | 14 March 2015, 00:27:39 UTC |
| d8b399b | Indraniel Das | 13 March 2015, 23:26:54 UTC | + apply @nnutter 6th recommendation (PR 557) - just directly apply skip_all. | 13 March 2015, 23:29:32 UTC |
| 57a5773 | Indraniel Das | 13 March 2015, 23:24:22 UTC | + apply @nnutter 5th recommendation (PR 557) - use Genome::Sys::copy_file just to be consistent with the rest of system. | 13 March 2015, 23:29:32 UTC |
| 8e56aa4 | Indraniel Das | 13 March 2015, 22:58:38 UTC | + apply @nnutter 4th recommendation (PR 557) - be paranoid -- add $ on the substitution regexp. | 13 March 2015, 23:29:31 UTC |
| f2398f3 | Indraniel Das | 13 March 2015, 22:53:30 UTC | + apply @nnutter 3rd recommendation (PR 557) - abstract away some duplicated code. @nnutter proposed this to be '_find_bin', I've changed it to '_bin_dir'. | 13 March 2015, 23:29:30 UTC |
| 033566c | Indraniel Das | 13 March 2015, 22:31:32 UTC | + apply @nnutter 2nd recommendation (PR 557) - use 'Integer' instead of 'Text' for the max mem parameter specification. Additionally mention in the help string, that the parameter needs to be specified in 'bytes' | 13 March 2015, 23:29:30 UTC |
| b552e5c | Indraniel Das | 13 March 2015, 22:26:37 UTC | + apply @nnutter 1st recommendation (PR 557) - use 'FilePath' instead of 'Text' for the params that take in file parmeters | 13 March 2015, 23:29:17 UTC |
| 512735f | Susanna Siebert | 13 March 2015, 18:30:03 UTC | fix help_detail links to point to correct anchor | 13 March 2015, 18:30:03 UTC |
| e62bed3 | Nathaniel Nutter | 13 March 2015, 18:22:31 UTC | use open_file_for_reading instead of IO::File Use `open_file_for_reading` instead of `IO::File->new` to get "free" validation that file was opened for reading. | 13 March 2015, 18:22:31 UTC |
| 448cf32 | Nathaniel Nutter | 13 March 2015, 18:19:25 UTC | pass around a hash instead of an array Using a hash is a more explicit than relying on the position in the array (with or without sorting). | 13 March 2015, 18:19:25 UTC |
| 787cb6f | Nathaniel Nutter | 13 March 2015, 18:11:09 UTC | use try instead of eval for proper scoping of $@ | 13 March 2015, 18:11:09 UTC |
| 9f9bd8d | Anthony Brummett | 13 March 2015, 17:15:53 UTC | Avoid an additional error when we can't connect to the logging DB The PostgreSQL error message can contain the server name in double quotes, which messes up building the string to be eval-ed, which generates an error about a runaway string. This escapes those quotes. | 13 March 2015, 17:15:53 UTC |
| 83865e2 | Anthony Brummett | 13 March 2015, 14:34:00 UTC | Fix DateTime calculation involving DST Builds were failing on Mar 13 between 2 and 3AM. _default_archive_after_time() adds 1 year to the current time. The 2016 DST changeover will happen on Mar 13, so 13 Mar 2016 2:45:00 won't exist. The error would also occur for any allocations created on Feb 29th. This change adds an equivalent number of seconds, which DateTime allows, and automatically adjusts for time changes. One downside is that when there's a Feb 29th between "now" and the calculated date, you'll technically have 1 day less than a year before it's archived. The alternative is to use DateTime's "floating" timezone (https://metacpan.org/pod/DateTime#Making-Things-Simple) which allows the calculation to produce an invalid date in the local timezone, but this seems more hacky. | 13 March 2015, 14:34:00 UTC |
| 73b488f | APipe Tester | 13 March 2015, 12:18:45 UTC | Updated `gmt` tab completion. | 13 March 2015, 12:18:45 UTC |
| 4ffb7e9 | APipe Tester | 13 March 2015, 12:17:57 UTC | Updated `genome` tab completion. | 13 March 2015, 12:17:57 UTC |
| d960702 | APipe Tester | 13 March 2015, 12:16:13 UTC | Updated class browser cache. | 13 March 2015, 12:16:13 UTC |
| d4988c4 | Eddie Belter | 12 March 2015, 23:53:35 UTC | InstData Generate: moar update help doc | 12 March 2015, 23:53:35 UTC |
| f64fb53 | Eddie Belter | 12 March 2015, 23:43:49 UTC | InstDAta Import: rename entity command generator | 12 March 2015, 23:43:49 UTC |
| d1de83c | Nathaniel Nutter | 12 March 2015, 23:15:54 UTC | fix typo | 12 March 2015, 23:15:54 UTC |
| 0c072db | Nathaniel Nutter | 12 March 2015, 23:13:03 UTC | support importing "new" Nimblegen capture/primary split bed files Add support for importing Nimblegen capture_targets/primary_targets split bed files. This feature was requested in [RT#104532][1]. [1]: https://rt.gsc.wustl.edu/Ticket/Display.html?id=104532 | 12 March 2015, 23:13:03 UTC |
| 48d7c2f | Allison Penner Regier | 12 March 2015, 21:16:03 UTC | Merge pull request #502 from tabbott/picard-refactor Picard refactoring | 12 March 2015, 21:16:03 UTC |
| d11a9d5 | Feiyu Du | 12 March 2015, 19:48:02 UTC | Merge pull request #407 from gsanders/recreate_per_lane_bam Recreate per-lane bams on demand (and delete them when done) | 12 March 2015, 19:48:02 UTC |
| daf800d | Jason Walker | 12 March 2015, 18:21:48 UTC | Make cummerbund an optional part of the workflow. | 12 March 2015, 18:21:48 UTC |
| e4db0b8 | Avinash Ramu | 12 March 2015, 17:05:03 UTC | update test db snapshot | 12 March 2015, 17:05:03 UTC |
| e38adde | Avinash Ramu | 12 March 2015, 15:18:50 UTC | Merge remote-tracking branch 'origin' into somaticfilter_workflow | 12 March 2015, 15:18:50 UTC |
| 7576045 | Indraniel Das | 11 March 2015, 22:44:18 UTC | Revert "+ bypass the test on the CI server" This reverts commit 9b961f1496ae03efff161f70f8a29cf1f896eee5. I'm trying out @brummett's & @nnutter's "Test Database Template" as described on TGI's confluence server. | 11 March 2015, 22:44:18 UTC |
| 9b961f1 | Indraniel Das | 11 March 2015, 22:05:14 UTC | + bypass the test on the CI server - this test relies on data that available only in TGI's production setting | 11 March 2015, 22:05:14 UTC |
| 587ff67 | Eddie Belter | 11 March 2015, 19:53:56 UTC | Merge pull request #553 from ebelter/genotype-concordance-users GMT Genotype CC: add users to VCF result | 11 March 2015, 19:53:56 UTC |
| 7ea4a62 | Eddie Belter | 11 March 2015, 19:47:22 UTC | Merge pull request #551 from ebelter/allpaths Allpaths: sanitize library names befroe writing to csv | 11 March 2015, 19:47:22 UTC |
| 57b6448 | Gabriel Sanderson | 11 March 2015, 18:50:48 UTC | pluralize _lock_per_lane_alignment | 11 March 2015, 18:50:48 UTC |
| 14b556d | Indraniel Das | 11 March 2015, 17:07:09 UTC | + adjust the models used for the test - this model was successfully identified as using Mix 2 and is based on the correct human only reference. | 11 March 2015, 17:30:11 UTC |
| 30d75d4 | Indraniel Das | 11 March 2015, 17:05:21 UTC | + remove the use_ok test - this is an autoloaded class. Test 3, the call to the create method on the class, will account for the module's existence. | 11 March 2015, 17:30:10 UTC |
| b05cad9 | Indraniel Das | 11 March 2015, 17:00:18 UTC | + suppress stdout from bowtie2-build index generation - this makes the output commands easier to see for the user. The index stats shown in stdout don't affect the index files that are generated. stderr will still be shown on the console screen in case if anything goes amiss. | 11 March 2015, 17:30:09 UTC |
| 16cbb33 | Indraniel Das | 11 March 2015, 16:29:35 UTC | + remove DB::single | 11 March 2015, 17:30:09 UTC |
| 4102217 | Indraniel Das | 11 March 2015, 15:04:26 UTC | + use samtools1.2 - this is based on @iferguson90 recent work on debian packaging samtools version 1.1 and 1.2. unfortunately the usage of these newer samtools isn't fully integrated into the Genome tree. The installation scheme for the newer samtools (1.x) is different from earlier samtools installations (pre 1.x). I think @iferguson90 is already working on addressing the integration into Genome issue. As I needed to use these newer samtools within the context of the ERCC analysis, I've sorted of "homebrewed" its usage inside this tool, rather than interfering with @iferguson90's current work. We'll see how this works out during review. | 11 March 2015, 17:30:08 UTC |
| 6a1c758 | Indraniel Das | 11 March 2015, 14:10:36 UTC | + change algorithmic approach (bwa to bowtie) - using bowtie2 in a single-read way seems to give the desired results - using a unix "pipe" or "streaming" approach - this reduces the time to produce the desired alignment results | 11 March 2015, 17:30:08 UTC |
| d31a8d2 | Indraniel Das | 26 February 2015, 19:44:22 UTC | + add test script | 11 March 2015, 17:30:07 UTC |
| 67d6882 | Indraniel Das | 26 February 2015, 19:34:14 UTC | + suppress the read 2 alignment - is this a bug, or a conceptual misunderstanding? | 11 March 2015, 17:30:07 UTC |
| e6caa1f | Indraniel Das | 26 February 2015, 19:33:17 UTC | + add a copy savepoint - I need to save this intermediate TSV file to debug the R script. | 11 March 2015, 17:30:06 UTC |
| 468f93f | Indraniel Das | 26 February 2015, 19:31:03 UTC | + print out a nice summary entry | 11 March 2015, 17:30:05 UTC |
| c318020 | Indraniel Das | 26 February 2015, 19:28:13 UTC | + adjust option variables - In the Rscript, replace "--filename" with "--data", and introduce a "--output" option. I was getting confused between the data file variable and the output pdf variable. - Instead of making multiple pdf file, just make one pdf file named via the "--output" option. | 11 March 2015, 17:30:05 UTC |
| cc7754f | Indraniel Das | 26 February 2015, 18:43:32 UTC | + suppress ggplot2 loading warning messages - we're using a older version of ggplot2. This edition gives a lot of unnecessary warnings messages when loading the package library. Newer editions of ggplot2 have removed these display issues. This approach suppresses those warnings so the R script will work more "nicely" for the end users. | 11 March 2015, 17:30:04 UTC |
| 155c615 | Indraniel Das | 26 February 2015, 18:25:40 UTC | + make the Rscript exit nicely | 11 March 2015, 17:30:03 UTC |
| f5d02fd | Indraniel Das | 26 February 2015, 18:24:56 UTC | + convert R script to use getopt instead of optparse - 'getopt' is installed in the current TGI R installation, 'optparse' isn't right now. | 11 March 2015, 17:30:03 UTC |
| 6dc20cc | Indraniel Das | 26 February 2015, 14:35:59 UTC | + return the remapped bam file, not the dir path | 11 March 2015, 17:30:02 UTC |
| f70141e | Indraniel Das | 26 February 2015, 06:40:46 UTC | + correctly end the package | 11 March 2015, 17:30:01 UTC |
| 2881cbf | Indraniel Das | 26 February 2015, 06:38:33 UTC | + make the ERCC fasta index before making the unmapped bam - generating the ERCC fasta index is faster than making the unmapped bam file. | 11 March 2015, 17:30:00 UTC |
| c1cb004 | Indraniel Das | 26 February 2015, 06:37:25 UTC | + correct ERRC fasta file example name - this file really exists on the file system. | 11 March 2015, 17:29:59 UTC |
| 1f102fd | Indraniel Das | 26 February 2015, 00:00:01 UTC | + fix option typos - default was misspelled. - the "example_values" values must be array refs. | 11 March 2015, 17:29:59 UTC |
| c6671d8 | Indraniel Das | 25 February 2015, 23:47:58 UTC | + remove commented out functions - they've now been placed into the GMT options section | 11 March 2015, 17:29:58 UTC |
| 5752cde | Indraniel Das | 25 February 2015, 23:46:13 UTC | + my first pass refactoring - I mostly broke up the original execute into multiple function calls for my easier comprehension of what's going on. | 11 March 2015, 17:29:58 UTC |
| f719fdc | Indraniel Das | 25 February 2015, 23:43:28 UTC | + initial raw version - I received these exact files from @jasonwalker80 | 11 March 2015, 17:29:57 UTC |
| 9d22a6d | Susanna Siebert | 11 March 2015, 17:28:29 UTC | Merge pull request #550 from susannasiebert/variant_reporting_vep CHANGELOG: Add option to variant reporting vep expert to use use short_name instead of name column in feature list. This keep the vep expert from failing if a feature list contains a special character, like semicolons. short_name is a required parameter so if your variant reporting plan file uses the vep expert you will need to add `short_name: 0` to the list of vep expert parameters. If you want to turn on the short_name option your need to add `short_name: 1` to the list of vep expert parameters. | 11 March 2015, 17:28:29 UTC |
| 51c00a1 | mkiwala | 11 March 2015, 17:15:29 UTC | Merge pull request #463 from mkiwala/update-determine-error Recognize new date format | 11 March 2015, 17:15:29 UTC |
| bd4ec3a | Nathaniel Nutter | 11 March 2015, 16:45:35 UTC | Merge pull request #554 from nnutter/test-fixes possible fix for apipe-ci/bats test failures | 11 March 2015, 16:45:35 UTC |
| cca6723 | Avinash Ramu | 11 March 2015, 16:18:18 UTC | Merge pull request #552 from gatoravi/site_sgms add site config for SGMS | 11 March 2015, 16:18:18 UTC |
| 188fe46 | Thomas B. Mooney | 11 March 2015, 15:35:18 UTC | Merge pull request #555 from tmooney/strip_priority_from_host_group Strip priorities from host-group parsing. | 11 March 2015, 15:35:18 UTC |
| 0cc1e8b | Thomas Mooney | 11 March 2015, 15:12:33 UTC | Strip priorities from host-group parsing. | 11 March 2015, 15:12:33 UTC |
| 3d5182c | Nathaniel Nutter | 11 March 2015, 05:54:23 UTC | possible fix for apipe-ci/bats test failures We've previously seen errors like this: (from function `cache_repo' in file test_helper.bash, line 34, from function `init_workspace' in file test_helper.bash, line 44, from function `setup' in test file submodule.bats, line 6) `init_workspace' failed with status 128 At the time Tom said he nuked the directories to fix it. The Git repos are being corrupted and I suspect it's because `tmpreaper` is trying to clean up. | 11 March 2015, 05:54:23 UTC |
| 2ef64da | Gabriel Sanderson | 10 March 2015, 22:30:28 UTC | Updated comment - we aren't avoiding NO_COMMIT in the code any longer. | 10 March 2015, 22:30:28 UTC |
| 45d7fa6 | Gabriel Sanderson | 10 March 2015, 22:04:40 UTC | Do not remove per-lane bam files with NO_COMMIT on. | 10 March 2015, 22:04:40 UTC |
| 681091c | Avinash Ramu | 10 March 2015, 21:56:48 UTC | specify right module | 10 March 2015, 21:56:48 UTC |
| b5acbd1 | Gabriel Sanderson | 10 March 2015, 21:47:12 UTC | Remove duplicate logic - resize_disk_allocation method. | 10 March 2015, 21:47:12 UTC |
| 287033b | Gabriel Sanderson | 10 March 2015, 21:20:11 UTC | Minor code review adjustments | 10 March 2015, 21:20:11 UTC |
| fd197c2 | Avinash Ramu | 10 March 2015, 17:57:35 UTC | add check for variant_files | 10 March 2015, 17:57:35 UTC |
| 50bd8d7 | Avinash Ramu | 10 March 2015, 17:56:55 UTC | use File::Spec | 10 March 2015, 17:56:55 UTC |
| 6dcc9ae | Eddie Belter | 10 March 2015, 17:55:33 UTC | Allpaths: sanitize lib name w/ sanitize_for_filesystem | 10 March 2015, 17:55:33 UTC |
| 45ac622 | Allison Penner Regier | 10 March 2015, 16:19:40 UTC | Merge pull request #540 from apregier/new_genome-env_option New genome-env option | 10 March 2015, 16:19:40 UTC |
| 3eac9bb | Avinash Ramu | 10 March 2015, 15:59:18 UTC | remove redundant param | 10 March 2015, 15:59:18 UTC |
| 6513a1b | Yevgeniy Gindin | 10 March 2015, 15:50:58 UTC | Addressed spaces in out_file name concerns by making the program fail early if space(s) are detected. | 10 March 2015, 15:50:58 UTC |
| 51e7916 | Susanna Siebert | 10 March 2015, 15:39:31 UTC | Only validate feature lists of short_name option is not set | 10 March 2015, 15:39:31 UTC |
| 2f1ac6c | Susanna Siebert | 10 March 2015, 15:38:38 UTC | Update error message to mention the short_name option | 10 March 2015, 15:38:38 UTC |
| a4c2fdb | Susanna Siebert | 10 March 2015, 15:34:53 UTC | check the first 100 lines, instead of just 10 | 10 March 2015, 15:34:53 UTC |
| d3b2a71 | Susanna Siebert | 10 March 2015, 15:33:50 UTC | Revert "remove feature list validation" This reverts commit 7d071a76e4bc62b5d2cb69f2dc4270a5eb4b1992. | 10 March 2015, 15:33:50 UTC |
| 914bc8f | Avinash Ramu | 10 March 2015, 04:58:38 UTC | add site config for SGMS | 10 March 2015, 04:58:38 UTC |
| 4795208 | Eddie Belter | 10 March 2015, 00:10:51 UTC | GMT Genotype CC: send qc build as sponsor/requestor to VCF result | 10 March 2015, 00:44:39 UTC |
| 69d594b | Eddie Belter | 10 March 2015, 00:10:24 UTC | GMT Genotype CC: update to __display_name__ | 10 March 2015, 00:10:24 UTC |
| f4e45b7 | Eddie Belter | 09 March 2015, 22:56:40 UTC | Allpaths: sanitize library names befroe writing to csv | 09 March 2015, 22:56:40 UTC |
| 79ca349 | Malachi Griffith | 09 March 2015, 22:38:40 UTC | Merge pull request #548 from malachig/master ClinSeq: update analysis now specifies cancer, misc, cosmic DBs | 09 March 2015, 22:38:40 UTC |
| b09e161 | Gabriel Sanderson | 09 March 2015, 22:05:53 UTC | Corrected lock location (no absolute paths) | 09 March 2015, 22:05:53 UTC |
| 7d071a7 | Susanna Siebert | 09 March 2015, 16:01:26 UTC | remove feature list validation | 09 March 2015, 21:54:45 UTC |
| 2fd4db5 | Susanna Siebert | 09 March 2015, 16:01:00 UTC | add option to vep expert to use short_name option in Genome::FeatureList::processed_bed_file_content | 09 March 2015, 21:54:45 UTC |
| 5976480 | Eddie Belter | 09 March 2015, 21:19:17 UTC | InstData Generate: update help doc | 09 March 2015, 21:19:17 UTC |
| 55e1ac0 | Malachi Griffith | 09 March 2015, 21:06:44 UTC | clin-seq: remove redundant use of default db id values and rename some variables for clarity | 09 March 2015, 21:06:44 UTC |
| 0955c4a | apregier | 09 March 2015, 20:32:19 UTC | Host and port will always come from either -i or test-db | 09 March 2015, 20:32:19 UTC |
| e3f9505 | apregier | 09 March 2015, 20:31:46 UTC | Always print host and port | 09 March 2015, 20:31:46 UTC |
| 5a70067 | Thomas Mooney | 09 March 2015, 18:32:54 UTC | Only filter undef properties from model creation. Omitting "undef" from the get() queries may pull back non-matching models, but including "undef" in create() calls may generate invalid hangoff objects. | 09 March 2015, 18:32:54 UTC |
| bcb7dbf | Eddie Belter | 09 March 2015, 17:31:05 UTC | Inst Data Generate Entity Cmds: do not get indivdual by upn | 09 March 2015, 17:31:05 UTC |
| b3103c7 | Yevgeniy Gindin | 09 March 2015, 17:28:03 UTC | Made suggested edits. | 09 March 2015, 17:28:03 UTC |
| 5c14d3a | apregier | 09 March 2015, 17:23:59 UTC | Add an option to not delete db when the shell goes away | 09 March 2015, 17:23:59 UTC |
| 7e4b64d | Susanna Siebert | 09 March 2015, 14:23:48 UTC | Merge pull request #543 from susannasiebert/variant_reporting_vaf Variant reporting vaf interpreter bugfix | 09 March 2015, 14:23:48 UTC |
| 7908975 | Thomas B. Mooney | 09 March 2015, 13:18:30 UTC | Merge pull request #539 from tmooney/queueing_for_everyone No longer hide build queue in docs. | 09 March 2015, 13:18:30 UTC |
