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diff --git a/README.org b/README.org index 2ab2229..0b6f8bc 100644 --- a/README.org +++ b/README.org @@ -1,11 +1,78 @@ * guix-bioinformatics IMPORTANT: this repository lives at https://git.genenetwork.org/guix-bioinformatics/! -Older packages have been moved to https://git.genenetwork.org/guix-bioinformatics-past/. -Over 400 bioinformatics packages for Guix that are used in https://genenetwork.org/ and some other places. +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. @@ -23,7 +90,7 @@ To easily use the packages from this repo, simply add it to your `channels` list 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-b0fa1dc --commit=b0fa1dc --channels=channels.scm + 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. @@ -32,6 +99,7 @@ The latest channel file that is used by our CI/CD you can find at https://ci.gen 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 |