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* 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+
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