* guix-bioinformatics

IMPORTANT: this repository lives at https://git.genenetwork.org/guix-bioinformatics/!

Over 300 older packages have been moved to https://git.genenetwork.org/guix-bioinformatics-past/. Check out the README to see what packages are there.

Over 300 bioinformatics packages for Guix that are used in https://genenetwork.org/ and some other places.
Mostly targetting genomics, pangenomics and genetics.

** Pangenome tools (pangenomes meta-package)

The =pangenomes= meta-package provides a comprehensive pangenomics toolkit:

| Tool           | Version      | Description                                    |
|----------------+--------------+------------------------------------------------|
| pggb           | 0.7.4        | PanGenome Graph Builder pipeline               |
| wfmash         | 0.14.0       | Whole-genome Fuzzy Mapping and Alignment        |
| seqwish        | 0.7.11       | Sequence graph induction from alignments        |
| smoothxg       | 0.8.2        | Graph normalization via partial order alignment  |
| odgi           | 0.9.0        | Optimized Dynamic Genome/Graph Implementation   |
| vg             | 1.72.0       | Variation graph toolkit                         |
| impg           | 0.4.1        | Implicit pangenome graph queries                |
| minimap2       | 2.28         | Fast pairwise aligner (from Guix upstream)      |
| bwa-mem2       | 2.3          | Burrows-Wheeler Aligner for short reads         |
| samtools       | 1.19         | SAM/BAM/CRAM manipulation (from Guix upstream)  |
| htslib         | 1.21         | HTSlib C library (from Guix upstream)           |
| bedtools       | 2.31.1       | Genome interval tools (from Guix upstream)      |
| bcftools       | 1.21         | VCF/BCF manipulation (from Guix upstream)       |
| vcflib         | 1.0.15       | VCF manipulation library and tools              |
| vcfbub         | 0.1.0        | VCF bubble popping                              |
| bandage-ng     | 2026.4.1     | Assembly graph visualizer (Qt6)                 |
| gfalook        | 0.1.0        | GFA visualization (odgi viz reimplementation)   |
| pafplot        | 0.1.0        | PAF alignment dotplot renderer                  |
| wally          | 0.7.1        | Structural variant visualization                |
| agc            | 2.1          | Assembled Genomes Compressor                    |
| cigzip         | 0.1.0        | CIGAR compression with tracepoints              |
| cosigt         | 0.1.7        | Pangenome haplotype genotyping                  |
| gfainject      | 0.1.0        | BAM-to-GAF graph injection                      |
| gafpack        | 0.0.0        | GAF coverage vector extraction                  |
| gfaffix        | 0.2.1        | Walk-preserving graph simplification            |
| gfautil        | 0.4.0        | GFA format utilities                            |
| fastga-rs      | 0.1.2        | Fast genome aligner (Rust)                      |
| fastix         | 0.1.0        | FASTA header prefix renaming (PanSN)            |
| kfilt          | 0.1.1        | K-mer filtering                                 |
| meryl          | 1.4.1        | K-mer counting and set operations               |
| miniprot       | 0.18         | Protein-to-genome aligner                       |
| pangene        | 1.1          | Gene-level pangenome analysis                   |
| rtg-tools      | 3.13         | VCF evaluation (vcfeval)                        |

** MEMPANG workshop (mempang-workshop meta-package)

Extends =pangenomes= with R plotting, Python, and general utilities
for the MEMPANG pangenome workshop tutorials:

| Category       | Packages                                             |
|----------------+------------------------------------------------------|
| R packages     | r-ggplot2, r-tidyverse, r-ape, r-ggtree, r-gggenes  |
| Python         | python, python-igraph, python-pycairo                |
| Utilities      | graphviz, gnuplot, parallel, pigz, wget, zstd, bc    |
| QC             | multiqc, mummer                                      |

** GeneNetwork packages

| Package              | Version      | Description                           |
|----------------------+--------------+---------------------------------------|
| genenetwork2         | 3.11         | GeneNetwork2 web application          |
| genenetwork3         | 0.1.0        | GeneNetwork3 REST API                 |
| gn-auth              | 1.0.1        | GN authentication service             |
| gn-guile             | 4.0.0        | Guile utilities for GN                |
| gn-libs              | 0.0.0        | Shared Python libraries               |
| gn-uploader          | 0.1.1        | Data uploader                         |
| gemma-wrapper        | 0.99.6       | GEMMA CLI wrapper                     |
| gemma-gn2            | 0.98.5       | GEMMA for GeneNetwork2                |
| genecup              | 1.8          | GeneCup literature mining             |

See Guix documentation and [[https://gitlab.com/pjotrp/guix-notes/blob/master/HACKING.org][Guix notes]] for installing and hacking Guix.

See [[https://github.com/franzos/awesome-guix][awesome guix]] for a list of other channels.

To easily use the packages from this repo, simply add it to your `channels` list in ~/.config/guix/channels.scm as described [[https://guix.gnu.org/manual/en/html_node/Channels.html][here]]:

#+BEGIN_SRC scheme
  ;; example channels.scm
  (list (channel
         (name 'guix-bioinformatics)
         (url "https://git.genenetwork.org/guix-bioinformatics")
         (branch "main")))
#+END_SRC

and run /guix pull/ like normal to update your software. E.g.

#+BEGIN_SRC sh
  guix pull --url=https://codeberg.org/guix/guix -p ~/opt/guix-bioinformatics  --channels=channels.scm
#+END_SRC

The channel file actually accesses https://git.genenetwork.org/guix-bioinformatics/tree/.guix-channel which pulls other channels and fixates the hashes. The commit hash b0fa1dc can be found from the guix you want to run with /guix -V/, it speeds up installation and makes it reproducible. Note that the upstream channel may override that version.

The latest channel file that is used by our CI/CD you can find at https://ci.genenetwork.org/channels.scm.

Channels are to maintain stability, the guix-bioinformatics channel depends on a specific commit of upstream Guix. So, it is recommended to isolate use of the guix-bioinformatics channel in a separate /guix pull/ profile, described [[https://issues.genenetwork.org/topics/guix-profiles][here]].

You can use the --tune=native switch to optimize performance when installing pangenome tools and gemma.

* Development tips

** Modify the load path

If you want to make changes to the packages in this repo you can set the GUIX_PACKAGE_PATH (or use the -L switch) to point to the root of this directory before running Guix. E.g.

#+BEGIN_SRC bash
      git clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git
      guix package -A cwl
#+END_SRC

** Override individual packages

The cheap and cheerful way of overriding a version of a package:

#+BEGIN_SRC scheme
    (use-modules (guix) (gnu packages emacs))

    (package
      (inherit emacs)
      (name "emacs-snapshot")
      (source "/path/to/some-file-or-directory.tar.gz"))
#+END_SRC

and then run:

: guix package --install-from-file=that-file.scm

* Substitute server

We run our own substitution server. Add the key to your machine as
root with

: guix archive --authorize < tux02-guix-substitutions-public-key.txt
: guix build -L ~/guix-bioinformatics/ --substitute-urls="https://cuirass.genenetwork.org https://ci.guix.gnu.org https://bordeaux.guix.gnu.org https://guix.genenetwork.org" hello

* Testing the build

All important packages are listed in manifest.scm.example. Test with

: guix build -L . -m manifest.scm.example --tune=native

* An important note on AI

The packages in guix-bioinformatics channel are generally written with the help of AI. Only the directory ./gnu/packages contains software that was crafted by hand without the help of AI.
The packages in this directory align with Guix policy and may be upstreamed to guix trunk.

* LICENSE

These package descriptions (so-called Guix expressions) are distributed by the same license as Guix, i.e. GPL3+