This is my fork of NixOS/nixpkgs. I've added a lot of software for personal use, and will eventually get around to cleaning it up and sending pull requests upstream. In the meantime, let me know if you're interested in anything here! Maybe you're the author, or you can't get it to work, or you got it working better, or whatever.
Personal dev workflow:
- Each package has its own
package-branch. - All
package-branches andmainstart from the latest release (currentlynixos/release-22.11) for binary cache compatibility. mainis just the upstream release with this custom README and all thepackage-branches merged periodically.
| Package | Needs maintainer | Builds & runs | PR opened upstream | Notes |
|---|---|---|---|---|
| gitit | ✔️ | TODO last update in 2021... become a maintainer? | ||
| motion | ❌ | |||
| mypaint | ❌ | |||
| trimal | ✔️ | TODO upgrade it and become a maintainer? | ||
| raxml | TODO does mine add anything to the existing one now? | |||
| blast | TODO is it worth packaging old versions too? | |||
| clustal-omega | ❌ | |||
| fasttree | TODO is it obsolete, or is veryfasttree different? | |||
| muscle | ❌ | ✔️ | l | |
| kallisto | ❌ | ✔️ | ||
| igv | ❌ | ✔️ | ||
| hmmer | ❌ | ✔️ | ||
| emboss | ❌ | ✔️ | ||
| diamond | ❌ | ✔️ | ||
| viennarna | ✔️ | |||
| aliview | ✔️ | |||
| R bioconductor packages + update script | ✔️ | ✔️ | ✔️ | |
| bitcoin unlimited | ❌ | ✔️ | ✔️ | Obsolete/dead? No longer contributing. |
| ape | with dependencies sdx and tclkit | |||
| argtable | what depends on this again? | |||
| bioperl | TODO: package each part in perl-packages.nix | |||
| biopython | ||||
| dendroscope | ✔️ | |||
| docopts | uses python to generate shell script CLI interfaces | |||
| etmtk | ✔️ | a task manager | ||
| fastme | ✔️ | |||
| fastx-toolkit | ✔️ | and the dependency libgtextutils | ||
| feba | TODO: package properly | |||
| figtree | ✔️ | |||
| gblocks | ✔️ | |||
| psiblast-exb | ✔️ | |||
| seqtrace | ✔️ | |||
| ortholang | ||||
| sunwait | ||||
| t-coffee | ||||
| tarql | ||||
| terminal-velocity | a CLI note-taking program similar to Notational Velocity | |||
| tidal | a Haskell library for live coding music (super fun!) | |||
| tidal-vim | ||||
| tnseq-transit | ||||
| xlsx2csv | ||||
| blastdbget | ||||
| cdhit | ||||
| crb-blast | ||||
| easel | ||||
| inparanoid | ||||
| justorthologs | ||||
| mcl | ||||
| mmseqs2 | ||||
| orthofinder | ||||
| treecl |