| 66d6a8f | Chris Miller | 07 December 2016, 15:08:04 UTC | Merge pull request #1642 from chrisamiller/master new copycat version requires bam-readcount v0.5, updated expected output files | 07 December 2016, 15:08:04 UTC |
| ba24d2e | Chris Miller | 07 December 2016, 05:05:27 UTC | new copycat version requires bam-readcount v0.5, updated expected output files | 07 December 2016, 05:05:59 UTC |
| a874a7d | APipe Tester | 06 December 2016, 13:18:13 UTC | Updated `gmt` tab completion. | 06 December 2016, 13:18:13 UTC |
| aeca5b7 | APipe Tester | 06 December 2016, 13:17:29 UTC | Updated `genome` tab completion. | 06 December 2016, 13:17:29 UTC |
| e63b098 | APipe Tester | 06 December 2016, 13:15:44 UTC | Updated class browser cache. | 06 December 2016, 13:15:44 UTC |
| 61322c5 | Jason Walker | 05 December 2016, 18:40:49 UTC | Merge pull request #1639 from jasonwalker80/config_disk_group_unarchive Use config to resolve disk group for unarchives. | 05 December 2016, 18:40:49 UTC |
| b442dc9 | Thomas B. Mooney | 05 December 2016, 18:36:40 UTC | Merge pull request #1638 from tmooney/lockproxy_test_uses_above Use above for loading Genome in LockProxy.t | 05 December 2016, 18:36:40 UTC |
| 6e47dfe | Thomas B. Mooney | 05 December 2016, 18:36:33 UTC | Merge pull request #1632 from tmooney/print_lock_name_when_waiting_on_lock Debug message for the resource when locking. | 05 December 2016, 18:36:33 UTC |
| 8246943 | Thomas B. Mooney | 05 December 2016, 18:36:15 UTC | Merge pull request #1636 from tmooney/is_mounted_trusts_symlinks Trust that symlinks are mounted. | 05 December 2016, 18:36:15 UTC |
| c739a43 | Thomas B. Mooney | 05 December 2016, 18:36:01 UTC | Merge pull request #1629 from tmooney/exclude_alignment_metrics_from_default_solexa_lister Exclude alignment metrics from default Solexa lister. | 05 December 2016, 18:36:01 UTC |
| 2b11c93 | Thomas B. Mooney | 05 December 2016, 18:35:53 UTC | Merge pull request #1640 from tmooney/remove_phred Remove tools that depend on `phred`. | 05 December 2016, 18:35:53 UTC |
| 93ee34d | Jason Walker | 05 December 2016, 18:25:16 UTC | Merge pull request #1622 from jasonwalker80/update_igv_refnames Update IGV ref name example values. | 05 December 2016, 18:25:16 UTC |
| e8bfa77 | Jason Walker | 05 December 2016, 17:36:11 UTC | Use estimated kb for allocation. | 05 December 2016, 17:36:11 UTC |
| 501c628 | APipe Tester | 02 December 2016, 13:17:46 UTC | Updated `gmt` tab completion. | 02 December 2016, 13:17:46 UTC |
| 19321b1 | APipe Tester | 02 December 2016, 13:17:02 UTC | Updated `genome` tab completion. | 02 December 2016, 13:17:02 UTC |
| 6fd17b4 | APipe Tester | 02 December 2016, 13:14:57 UTC | Updated class browser cache. | 02 December 2016, 13:14:57 UTC |
| 2a63ace | Thomas B. Mooney | 01 December 2016, 23:00:39 UTC | Remove tools that depend on `phred`. | 01 December 2016, 23:17:47 UTC |
| 5433da4 | Thomas B. Mooney | 01 December 2016, 19:41:07 UTC | Merge pull request #1637 from tmooney/remove_rdp Remove support for RDP. | 01 December 2016, 19:41:07 UTC |
| c604743 | Jason Walker | 01 December 2016, 19:28:03 UTC | Use config to resolve disk group for unarchives. | 01 December 2016, 19:28:03 UTC |
| e305e8d | Jason Walker | 01 December 2016, 17:54:10 UTC | Merge pull request #1634 from jasonwalker80/lookup_snvs_result SnvIndelReport standalone support | 01 December 2016, 17:54:10 UTC |
| 5dabb56 | Jason Walker | 01 December 2016, 16:41:06 UTC | Make target_gene_list and target_gene_list_name required and remove default. | 01 December 2016, 16:41:06 UTC |
| 2b5f8fb | Jason Walker | 01 December 2016, 16:39:49 UTC | Change order of operations for resolving annotated snvs vcf. Fail if shorcut does not work. | 01 December 2016, 16:39:49 UTC |
| d3be886 | Thomas B. Mooney | 01 December 2016, 16:18:33 UTC | Merge pull request #1635 from tmooney/use_db_for_breakannot Use Genome DB instead of hardcoded /gsc/ path. | 01 December 2016, 16:18:33 UTC |
| cd85786 | Thomas B. Mooney | 30 November 2016, 22:45:04 UTC | Use above for loading Genome in LockProxy.t | 30 November 2016, 22:45:04 UTC |
| d6aa6ea | Thomas B. Mooney | 30 November 2016, 22:12:11 UTC | Remove support for RDP. | 30 November 2016, 22:12:11 UTC |
| 73abdb3 | Thomas B. Mooney | 30 November 2016, 21:20:31 UTC | Trust that symlinks are mounted. | 30 November 2016, 21:20:31 UTC |
| 9ff84b4 | Thomas B. Mooney | 30 November 2016, 20:41:07 UTC | Use Genome DB instead of hardcoded /gsc/ path. | 30 November 2016, 20:41:07 UTC |
| 2eaf896 | Thomas B. Mooney | 30 November 2016, 14:57:52 UTC | Debug message for the resource when locking. This should make it easier to find out what we're waiting on when something else has the lock. This replaces the earlier pre-backend message that would output the entire contents of the file lock. * Can't use debug_message() here since we're not a UR::Object. * Genome::Logger might be better, but support for that isn't great. | 30 November 2016, 19:19:46 UTC |
| 6bf5853 | Jason Walker | 30 November 2016, 18:17:09 UTC | change precedence of SNV VCF lookup. Add correct user hash to command. | 30 November 2016, 18:17:09 UTC |
| e30f451 | Jason Walker | 30 November 2016, 02:55:26 UTC | inital attempt at looking up the result or shortcutting. | 30 November 2016, 02:55:26 UTC |
| c3c9b74 | Feiyu Du | 29 November 2016, 20:12:59 UTC | Merge pull request #1630 from dufeiyu/update_cletest Add PindelRegion region file feature list to CleTest | 29 November 2016, 20:12:59 UTC |
| a50942c | Feiyu Du | 29 November 2016, 17:37:33 UTC | Add PindelRegion region file feature list to CleTest | 29 November 2016, 17:37:33 UTC |
| f09971c | Feiyu Du | 23 November 2016, 20:08:46 UTC | Merge pull request #1628 from dufeiyu/update_cle Update CLE Test | 23 November 2016, 20:08:46 UTC |
| 71c29b9 | Thomas B. Mooney | 23 November 2016, 13:47:59 UTC | Exclude alignment metrics from default Solexa lister. When the LIMS was calculating these, they were quick lookups since they came as instrument data properties. Now that they're not, there's only the hacky "default_alignment_results" to get them. The question doesn't really make sense in a world where alignment can be done any number of ways. | 23 November 2016, 18:24:29 UTC |
| f34ac07 | Feiyu Du | 22 November 2016, 22:12:37 UTC | update CleTest with new processing profile and blessed builds/process | 22 November 2016, 22:12:37 UTC |
| 80af2cb | Thomas B. Mooney | 22 November 2016, 16:56:04 UTC | Merge pull request #1627 from tmooney/remove_bpdeluxe_module Remove top-level BPdeluxe.pm | 22 November 2016, 16:56:04 UTC |
| f071ff4 | APipe Tester | 22 November 2016, 13:18:26 UTC | Updated `gmt` tab completion. | 22 November 2016, 13:18:26 UTC |
| a15eed9 | APipe Tester | 22 November 2016, 13:17:43 UTC | Updated `genome` tab completion. | 22 November 2016, 13:17:43 UTC |
| c77af7a | APipe Tester | 22 November 2016, 13:16:13 UTC | Updated class browser cache. | 22 November 2016, 13:16:13 UTC |
| 87e6812 | Jason Walker | 21 November 2016, 20:56:58 UTC | Merge pull request #1621 from jasonwalker80/remove_instdata_limitation Remove imported restriction to assiging instrument data. | 21 November 2016, 20:56:58 UTC |
| 35ac6e1 | Jason Walker | 21 November 2016, 19:52:10 UTC | update sort order based on relevance. | 21 November 2016, 19:52:10 UTC |
| 6507ebe | Thomas B. Mooney | 21 November 2016, 19:26:54 UTC | Merge pull request #1617 from tmooney/bwamem_converts_fragment_bam_to_fastq_properly BWA-MEM: Only pass parameter for paired FASTQs if "-p" flag used. | 21 November 2016, 19:26:54 UTC |
| 3a2f9f1 | Jason Walker | 21 November 2016, 19:22:30 UTC | Add hg38 and mm10 as example values for IGV references. | 21 November 2016, 19:22:30 UTC |
| cea8865 | Jason Walker | 21 November 2016, 19:13:53 UTC | Remove imported restriction to assiging instrument data. | 21 November 2016, 19:13:53 UTC |
| 2d48d2d | Thomas B. Mooney | 21 November 2016, 19:10:04 UTC | Merge pull request #1618 from tmooney/remove_spurious_whitespace_in_jobiterator Remove spurious whitespace in regex. | 21 November 2016, 19:10:04 UTC |
| 9214d38 | Thomas B. Mooney | 21 November 2016, 19:09:50 UTC | Merge pull request #1615 from tmooney/remove_gmt_kmer Remove old `gmt kmer` tree. | 21 November 2016, 19:09:50 UTC |
| f46646e | Thomas B. Mooney | 21 November 2016, 19:09:43 UTC | Merge pull request #1612 from tmooney/use_testdata_for_adapter_file Use test input for adapter file instead of hardcoded path. | 21 November 2016, 19:09:43 UTC |
| 4204697 | Thomas B. Mooney | 21 November 2016, 19:09:26 UTC | Merge pull request #1609 from tmooney/analysis_project_view_includes_inactive_configs Add separate flag to control display of inactive configs. | 21 November 2016, 19:09:26 UTC |
| d602fe1 | Thomas B. Mooney | 21 November 2016, 19:09:15 UTC | Merge pull request #1604 from tmooney/remove_park_beta Remove "Park" beta. | 21 November 2016, 19:09:15 UTC |
| 656707d | Thomas B. Mooney | 21 November 2016, 18:41:06 UTC | Remove top-level BPdeluxe.pm There is another copy at: Genome/Model/Tools/Predictor/BPdeluxe.pm | 21 November 2016, 18:41:06 UTC |
| 5058219 | Thomas B. Mooney | 17 November 2016, 18:27:57 UTC | Merge pull request #1620 from tmooney/correct_operator_precedence_in_test_builder Test::Builder: Don't return before evaluating the entire expression. | 17 November 2016, 18:27:57 UTC |
| 44e515d | Thomas B. Mooney | 17 November 2016, 18:26:56 UTC | Merge branch 'master' into remove_park_beta Conflicts: lib/perl/Genome/Model/GenePrediction/Command/Pap/Blast/BladeBlastBatcher.pm lib/perl/Genome/Model/GenePrediction/Command/Pap/KEGGScan/RunKeggScan.pm | 17 November 2016, 18:26:56 UTC |
| 3052740 | Thomas B. Mooney | 17 November 2016, 18:24:28 UTC | Merge pull request #1611 from tmooney/configurable_memory_limit_for_picard Make Java heap and permgen configurable for calling Picard. | 17 November 2016, 18:24:28 UTC |
| 5b8e1fe | Thomas B. Mooney | 17 November 2016, 18:24:01 UTC | Merge pull request #1619 from tmooney/sr_avoid_calling_each_while_inserting_into_hash Avoid using `each()` in loop where we insert into the hash. | 17 November 2016, 18:24:01 UTC |
| ff05d0a | Thomas B. Mooney | 16 November 2016, 23:42:35 UTC | Don't return before evaluating the entire expression. This module really shouldn't be in the repository to begin with... but as long as we're supporting old systems it shall remain. | 16 November 2016, 23:42:35 UTC |
| c811b39 | Thomas B. Mooney | 16 November 2016, 22:37:56 UTC | Avoid using `each()` in loop where we insert into the hash. Newer Perl's provide this warning: > Use of each() on hash after insertion without resetting hash iterator > results in undefined behavior | 16 November 2016, 22:37:56 UTC |
| 9f9c7bd | Thomas B. Mooney | 16 November 2016, 22:24:29 UTC | Remove spurious whitespace in regex. Perl 5.22 warned of an unescaped "{". Seems like it was a quantifier gone wrong. The history of this module is obscured, though. | 16 November 2016, 22:24:29 UTC |
| 7399b54 | Thomas B. Mooney | 16 November 2016, 14:30:57 UTC | Only pass parameter for paired output if "-p" flag used in bwa-mem. | 16 November 2016, 14:30:57 UTC |
| 91fd81b | Joshua McMichael | 15 November 2016, 16:11:55 UTC | Merge pull request #1593 from tmooney/bugfix_coverage_html_table_structure Coverage Report: Use a wrapping <div> for the hiding. Apply dataTables to the <table>. | 15 November 2016, 16:11:55 UTC |
| 5413417 | APipe Tester | 11 November 2016, 13:18:03 UTC | Updated `gmt` tab completion. | 11 November 2016, 13:18:03 UTC |
| 91d6132 | APipe Tester | 11 November 2016, 13:17:20 UTC | Updated `genome` tab completion. | 11 November 2016, 13:17:20 UTC |
| 8667111 | APipe Tester | 11 November 2016, 13:15:46 UTC | Updated class browser cache. | 11 November 2016, 13:15:46 UTC |
| 9418845 | Thomas B. Mooney | 10 November 2016, 22:40:36 UTC | Merge pull request #1616 from tmooney/remove_obsolete_utilities Remove various "Genome::Utility" entries that seem disused. | 10 November 2016, 22:40:36 UTC |
| 558bd96 | Thomas B. Mooney | 10 November 2016, 16:52:41 UTC | Merge pull request #1610 from tmooney/make_it_possible_to_disable_fs_caching Make it possible to disable local filesystem caching. | 10 November 2016, 16:52:41 UTC |
| 1428b3f | Thomas B. Mooney | 10 November 2016, 16:51:56 UTC | Merge pull request #1613 from tmooney/remove_gmt_analysis_indels_dbsnpconcord Remove old `gmt analysis indels dbsnp-concord` tool. | 10 November 2016, 16:51:56 UTC |
| 31f52ca | Thomas B. Mooney | 10 November 2016, 16:51:43 UTC | Merge pull request #1614 from tmooney/remove_disabled_gmt_bedtools_coverage Remove old tool that was "disabled" in 2010. | 10 November 2016, 16:51:43 UTC |
| f9dd0b3 | APipe Tester | 10 November 2016, 13:18:52 UTC | Updated `gmt` tab completion. | 10 November 2016, 13:18:52 UTC |
| fd779ee | APipe Tester | 10 November 2016, 13:18:04 UTC | Updated `genome` tab completion. | 10 November 2016, 13:18:04 UTC |
| 07f318b | APipe Tester | 10 November 2016, 13:16:24 UTC | Updated class browser cache. | 10 November 2016, 13:16:24 UTC |
| 302c831 | Thomas B. Mooney | 09 November 2016, 22:57:13 UTC | Remove Genome::Utility::BioPerl tree. | 09 November 2016, 22:57:13 UTC |
| 786e7fc | Thomas B. Mooney | 09 November 2016, 22:52:15 UTC | Remove "Editor" Utility. I heartell this idea never got put to full use. | 09 November 2016, 22:52:15 UTC |
| d22285a | Thomas B. Mooney | 09 November 2016, 22:47:23 UTC | Remove TranscriptHelper Utility. | 09 November 2016, 22:47:23 UTC |
| 8675712 | Thomas B. Mooney | 09 November 2016, 22:43:22 UTC | Remove 454TrimFile Utility and tools. | 09 November 2016, 22:43:22 UTC |
| f3fc70c | Thomas B. Mooney | 09 November 2016, 22:41:56 UTC | Remove SeqcleanReport Utility and tool. | 09 November 2016, 22:41:56 UTC |
| da92807 | Thomas B. Mooney | 09 November 2016, 22:39:44 UTC | Remove Genome::Utility::IAValidate. | 09 November 2016, 22:39:44 UTC |
| ab7bf1d | Thomas B. Mooney | 09 November 2016, 22:28:47 UTC | Remove `gmt kmer` tree. | 09 November 2016, 22:28:47 UTC |
| 6a4de1d | Thomas B. Mooney | 09 November 2016, 21:58:55 UTC | Remove old tool that was "disabled" in 2010. | 09 November 2016, 21:58:55 UTC |
| fd1e430 | Thomas B. Mooney | 09 November 2016, 21:52:22 UTC | Remove old tool with nonexistent path. | 09 November 2016, 21:52:22 UTC |
| d3f8fb0 | Thomas B. Mooney | 09 November 2016, 21:23:09 UTC | Use test input for adapter file instead of hardcoded path. | 09 November 2016, 21:28:45 UTC |
| d48cd9a | Thomas B. Mooney | 09 November 2016, 19:36:35 UTC | Merge pull request #1605 from tmooney/retire_geneprediction_bacterial_models Retire GenePrediction::Bacterial model type. | 09 November 2016, 19:36:35 UTC |
| 7ddc365 | Thomas B. Mooney | 09 November 2016, 19:36:26 UTC | Merge pull request #1607 from tmooney/reduce_gsc_references Eliminate "low-hanging" /gsc/ references. | 09 November 2016, 19:36:26 UTC |
| 82b2d77 | Thomas B. Mooney | 09 November 2016, 19:32:20 UTC | Make Java heap and permgen configurable for calling Picard. | 09 November 2016, 19:32:20 UTC |
| 82f78c3 | Thomas B. Mooney | 08 November 2016, 19:36:37 UTC | Make it possible to disable local filesystem caching. Set config to empty string or non-existent location to disable cache. (This will fall back to original location if cache is temporarily unavailable as well.) | 08 November 2016, 19:36:37 UTC |
| 2ced190 | Thomas B. Mooney | 08 November 2016, 15:33:38 UTC | Add separate flag to control display of inactive configs. Closes #1608. | 08 November 2016, 15:33:38 UTC |
| 33ec279 | APipe Tester | 03 November 2016, 12:18:04 UTC | Updated `gmt` tab completion. | 03 November 2016, 12:18:04 UTC |
| a46368f | APipe Tester | 03 November 2016, 12:17:22 UTC | Updated `genome` tab completion. | 03 November 2016, 12:17:22 UTC |
| f061473 | APipe Tester | 03 November 2016, 12:15:49 UTC | Updated class browser cache. | 03 November 2016, 12:15:49 UTC |
| c6e359c | Chris Miller | 03 November 2016, 05:15:37 UTC | Merge pull request #1601 from chrisamiller/master fixing issues with target-region filtering, header, and indels | 03 November 2016, 05:15:37 UTC |
| c5b3cca | Chris Miller | 02 November 2016, 19:24:24 UTC | sanitizing strings and using build instead of model for target region | 02 November 2016, 19:24:38 UTC |
| f3ddc7b | Chris Miller | 21 October 2016, 21:42:35 UTC | fixing header on output files | 02 November 2016, 19:24:37 UTC |
| 63cb4e0 | Chris Miller | 21 October 2016, 17:33:25 UTC | fixing several issues with target-region filtering and indels | 02 November 2016, 19:24:37 UTC |
| a4d23dd | Thomas B. Mooney | 02 November 2016, 15:37:25 UTC | Merge pull request #1606 from tmooney/reduce_gscuser_references Reduce "gscuser" references. | 02 November 2016, 15:37:25 UTC |
| d97229f | Thomas B. Mooney | 02 November 2016, 15:21:48 UTC | Merge pull request #1603 from tmooney/use_annotation_db_for_gene_targets_file_in_cnview_tests Use the annotation DB instead of a hardcoded path for targets file. | 02 November 2016, 15:21:48 UTC |
| c13a2f7 | Susanna Kiwala | 02 November 2016, 15:18:13 UTC | Merge pull request #1598 from susannasiebert/snv_indel_report Also look for the snv_indel_report_clean_unfiltered_file and snv_indel_report_clean_filtered_file by the subject's name | 02 November 2016, 15:18:13 UTC |
| 45243c6 | Susanna Kiwala | 02 November 2016, 15:17:51 UTC | Merge pull request #1588 from susannasiebert/clinseq_failure Make sure the $tumor_subject_common_name is defined before regexing it | 02 November 2016, 15:17:51 UTC |
| 9bf7b61 | Thomas B. Mooney | 01 November 2016, 21:39:10 UTC | Remove obsolete Workflow callback. | 01 November 2016, 21:39:10 UTC |
| bb6aab9 | Thomas B. Mooney | 01 November 2016, 21:36:19 UTC | Remove defunct command. | 01 November 2016, 21:36:19 UTC |
| b74ea69 | Thomas B. Mooney | 01 November 2016, 21:34:44 UTC | We already broke /gsc/bin/perl. | 01 November 2016, 21:34:44 UTC |
| 9a01f43 | Thomas B. Mooney | 01 November 2016, 21:31:37 UTC | Make default simply /var/log/. In practice we don't write to this directory anyway. | 01 November 2016, 21:31:37 UTC |
| 391fcad | Thomas B. Mooney | 01 November 2016, 21:28:42 UTC | Reduce path to just snapshot number. | 01 November 2016, 21:28:42 UTC |
