Age | Commit message (Collapse) | Author | |
---|---|---|---|
2022-01-25 | add bgz support and fix nested compression support | Justin Bedo | |
2021-12-18 | update dbNSFP hashes | Justin Bedo | |
these have changed‽ | |||
2021-10-29 | treewide reformatting and simplification | Justin Bedo | |
- simplify with statix - reformat with nixpkgs-fmt | |||
2021-02-08 | refactor slurm implementation to allow for overlays | Justin Bedo | |
2020-12-21 | snpeff: dbnsfp update | Justin Bedo | |
2020-11-18 | add encode blacklist to references | Justin Bedo | |
2020-11-18 | switch to unchecked ADTs | Justin 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. | |||
2020-06-23 | qsub,slurm: fix string escaping bug | Justin 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. | |||
2020-02-14 | add gdrive downloader | Justin Bedo | |
- fetch dbNSFP automatically via gdrive.pl | |||
2019-11-29 | snpeff: GRCh37.87 -> GRCh37.75 | Justin Bedo | |
2019-09-25 | grch37: add dbsnp | Justin Bedo | |
2019-09-25 | grch38.31 → grch38.32 | Justin Bedo | |
2019-09-25 | add grch37 | Justin Bedo | |
2019-07-08 | ensembl: init gtf and gff3 | Justin Bedo | |
2019-07-08 | ensembl: abstract version | Justin Bedo | |
2019-06-18 | slurm: fix bug with srun | Justin Bedo | |
salloc must call srun to actually launch job on execution node rather than submission node | |||
2019-06-12 | grcm38: fix typo in name of ensembl transcripts | Justin Bedo | |
2019-06-11 | qsub: parameterise the path to PBS utils | Justin Bedo | |
2019-06-11 | references: fix file mode (remove executable flag) | Justin Bedo | |
2019-05-16 | slurm: renamed from sbatch | Justin Bedo | |
2019-05-16 | sbatch: allow path specification for salloc | Justin Bedo | |
2019-05-02 | shard-regex: split into separate file to fix exec issues | Justin Bedo | |
2019-05-02 | shard: missing file | Justin Bedo | |
2019-04-18 | sbatch: initial slurm implementation | Justin Bedo | |
2019-03-15 | add multicore passthru flag | Justin Bedo | |
2019-03-04 | qsub: fix bug | Justin Bedo | |
2019-03-01 | qsub: fix temporary directory cleanup | Justin Bedo | |
2019-02-15 | ref: missing pkg scope on gawk | Justin Bedo | |
2019-02-06 | qsub: rename flags to qsubFlags to avoid collision | Justin Bedo | |
2019-02-06 | ref-grch38-snpeff-db: fix pkg scope | Justin Bedo | |
2019-02-06 | qsub: parameterise queue and allow arbitrary flags to be passed | Justin Bedo | |
2019-01-23 | stage: change to stdenvNoCC | Justin Bedo | |
2019-01-14 | qsub: fix bug in stderr redirection | Justin Bedo | |
2019-01-11 | ucscgenes: fix url to correct hg38 | Justin Bedo | |
2019-01-10 | ref: add UCSC gene annotations | Justin Bedo | |
2019-01-09 | large refactor | Justin Bedo | |
- use bionix.pkgs instead of nixpkgs - replace stdenv.mkDerivation with stage | |||
2019-01-08 | types: expose nix-adt | Justin Bedo | |
2019-01-08 | snpeff: init | Justin Bedo | |
2018-12-21 | qsub: capture stderr and stdout jointly | Justin Bedo | |
2018-12-20 | qsub: bugfix with printing jobid for debugging | Justin Bedo | |
2018-12-19 | qsub: echo out PBS_NODE_ID to ease debugging | Justin Bedo | |
2018-12-18 | qsub: refactor overriding | Justin Bedo | |
2018-12-11 | qsub: prefix directories to prevent cleanup deleting top level dir | Justin Bedo | |
2018-12-10 | qsub: fix $TMPDIR location | Justin Bedo | |
2018-11-26 | qsub: output non-retryable errors | Justin Bedo | |
2018-11-26 | qsub: let sleep timing be configurable | Justin Bedo | |
2018-11-26 | qsub: retry qsub if requested | Justin Bedo | |
2018-11-23 | qsub: update to check job_state field | Justin Bedo | |
2018-11-23 | qsub: be more specific with qstat polling | Justin Bedo | |
2018-11-14 | Add ensembl mouse transcriptome | Justin Bedo | |