bionix.git/lib, branch master Functional, highly-reproducible bioinformatics pipelines quip: init 2022-05-16T03:07:24+00:00 Justin Bedo cu@cua0.org 2022-05-16T02:46:12+00:00 2bd2c3958ed91ef3bbea2fc3e077a8c03a648a1b 






add bgz support and fix nested compression support
2022-01-25T01:03:45+00:00

Justin Bedo
cu@cua0.org

2022-01-25T01:03:45+00:00

173e7a758569796a91120379853b94f35dcc4a81












update dbNSFP hashes
2021-12-18T00:05:05+00:00

Justin Bedo
cu@cua0.org

2021-12-18T00:05:05+00:00

cef60e7a0dca226c045641c7a8cc53359c043168

these have changed‽





these have changed‽







treewide reformatting and simplification
2021-10-29T06:39:01+00:00

Justin Bedo
cu@cua0.org

2021-10-29T06:39:01+00:00

bac9248a5e08e8afdf5485a6e27cfe72e1ca5090

- simplify with statix
- reformat with nixpkgs-fmt





- simplify with statix
- reformat with nixpkgs-fmt







refactor slurm implementation to allow for overlays
2021-02-08T06:40:52+00:00

Justin Bedo
cu@cua0.org

2021-02-08T06:40:52+00:00

4f7f2770baecc5f72ca9e90d7996c0a1554bda1b












snpeff: dbnsfp update
2020-12-20T21:17:53+00:00

Justin Bedo
cu@cua0.org

2020-12-20T21:17:53+00:00

92d6a00f95b0cb7e0c643489c97109acdce196b9












add encode blacklist to references
2020-11-18T03:13:26+00:00

Justin Bedo
cu@cua0.org

2020-11-18T03:13:26+00:00

e4e46adf874a47a726f3f142c656ecaff9ee6cd3












switch to unchecked ADTs
2020-11-17T20:40:59+00:00

Justin Bedo
cu@cua0.org

2020-11-17T20:40:59+00:00

eede5717879062ef0cebde2a5718725e7afd17ca

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.





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.







qsub,slurm: fix string escaping bug
2020-06-23T07:28:19+00:00

Justin Bedo
cu@cua0.org

2020-06-23T07:28:00+00:00

7e5542eadad1db9271fe1d18b5682eacebadbf48

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.





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.







add gdrive downloader
2020-02-13T21:09:08+00:00

Justin Bedo
cu@cua0.org

2020-02-13T21:09:08+00:00

57ccba7da6feb46475f1ad58126a663356efe358

- fetch dbNSFP automatically via gdrive.pl





- fetch dbNSFP automatically via gdrive.pl