bionix.git/lib, branch masterFunctional, highly-reproducible bioinformatics pipelineshttps://vk3.wtf/cgit/bionix.git/atom/lib?h=master2022-05-16T03:07:24Zquip: init2022-05-16T03:07:24ZJustin Bedocu@cua0.org2022-05-16T02:46:12Zurn:sha1:2bd2c3958ed91ef3bbea2fc3e077a8c03a648a1badd bgz support and fix nested compression support2022-01-25T01:03:45ZJustin Bedocu@cua0.org2022-01-25T01:03:45Zurn:sha1:173e7a758569796a91120379853b94f35dcc4a81update dbNSFP hashes2021-12-18T00:05:05ZJustin Bedocu@cua0.org2021-12-18T00:05:05Zurn:sha1:cef60e7a0dca226c045641c7a8cc53359c043168
these have changed‽
treewide reformatting and simplification2021-10-29T06:39:01ZJustin Bedocu@cua0.org2021-10-29T06:39:01Zurn:sha1:bac9248a5e08e8afdf5485a6e27cfe72e1ca5090
- simplify with statix
- reformat with nixpkgs-fmt
refactor slurm implementation to allow for overlays2021-02-08T06:40:52ZJustin Bedocu@cua0.org2021-02-08T06:40:52Zurn:sha1:4f7f2770baecc5f72ca9e90d7996c0a1554bda1bsnpeff: dbnsfp update2020-12-20T21:17:53ZJustin Bedocu@cua0.org2020-12-20T21:17:53Zurn:sha1:92d6a00f95b0cb7e0c643489c97109acdce196b9add encode blacklist to references2020-11-18T03:13:26ZJustin Bedocu@cua0.org2020-11-18T03:13:26Zurn:sha1:e4e46adf874a47a726f3f142c656ecaff9ee6cd3switch to unchecked ADTs2020-11-17T20:40:59ZJustin Bedocu@cua0.org2020-11-17T20:40:59Zurn:sha1: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.
qsub,slurm: fix string escaping bug2020-06-23T07:28:19ZJustin Bedocu@cua0.org2020-06-23T07:28:00Zurn:sha1:7e5542eadad1db9271fe1d18b5682eacebadbf48
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.
add gdrive downloader2020-02-13T21:09:08ZJustin Bedocu@cua0.org2020-02-13T21:09:08Zurn:sha1:57ccba7da6feb46475f1ad58126a663356efe358
- fetch dbNSFP automatically via gdrive.pl