Age | Commit message (Collapse) | Author | |
---|---|---|---|
2020-11-17 | implement overlays | Justin Bedo | |
2020-11-16 | sambamba: init | Justin Bedo | |
2020-11-02 | star: init | Justin Bedo | |
2020-06-27 | whisper: init 2.0 | Justin Bedo | |
2020-04-22 | fix error message for linkOutputs | Justin Bedo | |
2020-03-27 | pipe now part of nixpkgs | Justin Bedo | |
2020-02-14 | add gdrive downloader | Justin Bedo | |
- fetch dbNSFP automatically via gdrive.pl | |||
2020-02-09 | lastal: init | Justin Bedo | |
2019-12-18 | add exec'' | Justin Bedo | |
2019-12-18 | lumpy: init | Justin Bedo | |
2019-12-17 | delly: init | Justin Bedo | |
2019-12-16 | manta: init | Justin Bedo | |
2019-09-06 | xenomapper: init | Justin Bedo | |
2019-08-15 | qsub: fix broken qsub tree | Justin Bedo | |
2019-08-15 | hisat2: init | Justin Bedo | |
2019-08-15 | SNVer: init 0.5.3 | Justin Bedo | |
2019-07-26 | make stripping more liberal | Justin Bedo | |
Update the regex so that /nix/store* prefix doesn't have to match. To make sure we aren't overly general, we strip only bionix stages (i.e., -bionix suffix has to be present in the hash). | |||
2019-07-08 | linkOutputs: refactor output linking expression | Justin Bedo | |
The existing linkDrv only has a singular output, making it difficult to separate the various types of output. The new functionality replaces the old with attribute sets defining the outputs. The old linkDrv is deprecated. | |||
2019-07-03 | octopus: initial functions | 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 | |||
2019-06-14 | slurm,qsub: update to allow chaining of execution engines | Justin Bedo | |
Previously exec was redefined to defer to slurm/pbs for execution. This did not chain the previous exec, meaning you couldn't chain execs. | |||
2019-06-11 | qsub: parameterise the path to PBS utils | Justin Bedo | |
2019-06-11 | slurm: allow salloc path to be overridden in stage calls | Justin Bedo | |
salloc was missing from defaults, preventing overriding of salloc path for each stage. | |||
2019-06-06 | Merge branch 'master' of https://github.com/PapenfussLab/bionix | l-d-s | |
2019-06-04 | strip: handle non-buildCommand based stages | Justin Bedo | |
2019-05-22 | Unested picard-markDuplicates. | l-d-s | |
2019-05-16 | slurm: renamed from sbatch | Justin Bedo | |
2019-05-16 | stage: fix multicore tagging to work with derivation overriding | Justin Bedo | |
2019-05-14 | strip: remove store paths from outputs to minimise closures | Justin Bedo | |
2019-05-02 | shard-regex: split into separate file to fix exec issues | Justin Bedo | |
2019-05-02 | shard: Implement some basic sharding for FQ files | Justin Bedo | |
2019-05-01 | Add fastp. | l-d-s | |
2019-04-18 | sbatch: initial slurm implementation | Justin Bedo | |
2019-04-17 | snap: init | Justin Bedo | |
2019-04-12 | minimap2: init | Justin Bedo | |
2019-04-07 | update stage names to include bionix- prefix | Justin Bedo | |
2019-03-15 | add multicore passthru flag | Justin Bedo | |
2019-03-01 | ascat: init | Justin Bedo | |
2019-02-06 | qsub: rename flags to qsubFlags to avoid collision | 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 | |
2019-01-10 | facets: init | Justin Bedo | |
2019-01-10 | cnvkit: init | Justin Bedo | |
2019-01-09 | large refactor | Justin Bedo | |
- use bionix.pkgs instead of nixpkgs - replace stdenv.mkDerivation with stage | |||
2019-01-09 | split/join/each: introduce functions for splitting/joining drvs | Justin Bedo | |
2019-01-08 | snpeff: init | Justin Bedo | |
2018-12-19 | bionix: export nixpkgs.lib as bionix.lib | Justin Bedo | |
2018-12-19 | link: introduce high-level linking functions | Justin Bedo | |
2018-12-18 | pipe: fix bug | Justin Bedo | |
2018-12-18 | pipe: reverse function composition | Justin Bedo | |