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2021-02-08refactor slurm implementation to allow for overlaysJustin Bedo
2020-12-21snpeff: dbnsfp updateJustin Bedo
2020-11-18add encode blacklist to referencesJustin Bedo
2020-11-18switch to unchecked ADTsJustin Bedo
Checked ADTs are causing an issue with the new overlays. If an overlay that provides the entire tree is used, e.g.,: (self: super: super.slurm {}) then the result is unusable due to ADT type checking errors.
2020-06-23qsub,slurm: fix string escaping bugJustin Bedo
escapeShellArgs calls toString on the passed item, which for paths converts it to a string containing the full path outside the nix store. Avoid this by calling escapeShellArg on strings only.
2020-02-14add gdrive downloaderJustin Bedo
- fetch dbNSFP automatically via gdrive.pl
2019-11-29snpeff: GRCh37.87 -> GRCh37.75Justin Bedo
2019-09-25grch37: add dbsnpJustin Bedo
2019-09-25grch38.31 → grch38.32Justin Bedo
2019-09-25add grch37Justin Bedo
2019-07-08ensembl: init gtf and gff3Justin Bedo
2019-07-08ensembl: abstract versionJustin Bedo
2019-06-18slurm: fix bug with srunJustin Bedo
salloc must call srun to actually launch job on execution node rather than submission node
2019-06-12grcm38: fix typo in name of ensembl transcriptsJustin Bedo
2019-06-11qsub: parameterise the path to PBS utilsJustin Bedo
2019-06-11references: fix file mode (remove executable flag)Justin Bedo
2019-05-16slurm: renamed from sbatchJustin Bedo
2019-05-16sbatch: allow path specification for sallocJustin Bedo
2019-05-02shard-regex: split into separate file to fix exec issuesJustin Bedo
2019-05-02shard: missing fileJustin Bedo
2019-04-18sbatch: initial slurm implementationJustin Bedo
2019-03-15add multicore passthru flagJustin Bedo
2019-03-04qsub: fix bugJustin Bedo
2019-03-01qsub: fix temporary directory cleanupJustin Bedo
2019-02-15ref: missing pkg scope on gawkJustin Bedo
2019-02-06qsub: rename flags to qsubFlags to avoid collisionJustin Bedo
2019-02-06ref-grch38-snpeff-db: fix pkg scopeJustin Bedo
2019-02-06qsub: parameterise queue and allow arbitrary flags to be passedJustin Bedo
2019-01-23stage: change to stdenvNoCCJustin Bedo
2019-01-14qsub: fix bug in stderr redirectionJustin Bedo
2019-01-11ucscgenes: fix url to correct hg38Justin Bedo
2019-01-10ref: add UCSC gene annotationsJustin Bedo
2019-01-09large refactorJustin Bedo
- use bionix.pkgs instead of nixpkgs - replace stdenv.mkDerivation with stage
2019-01-08types: expose nix-adtJustin Bedo
2019-01-08snpeff: initJustin Bedo
2018-12-21qsub: capture stderr and stdout jointlyJustin Bedo
2018-12-20qsub: bugfix with printing jobid for debuggingJustin Bedo
2018-12-19qsub: echo out PBS_NODE_ID to ease debuggingJustin Bedo
2018-12-18qsub: refactor overridingJustin Bedo
2018-12-11qsub: prefix directories to prevent cleanup deleting top level dirJustin Bedo
2018-12-10qsub: fix $TMPDIR locationJustin Bedo
2018-11-26qsub: output non-retryable errorsJustin Bedo
2018-11-26qsub: let sleep timing be configurableJustin Bedo
2018-11-26qsub: retry qsub if requestedJustin Bedo
2018-11-23qsub: update to check job_state fieldJustin Bedo
2018-11-23qsub: be more specific with qstat pollingJustin Bedo
2018-11-14Add ensembl mouse transcriptomeJustin Bedo
2018-11-02kallisto: initJustin Bedo
2018-10-26init: cosmic & dbsnp for grch38Justin Bedo
2018-10-25Improve type safety of samtools-mergeJustin Bedo
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