diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 129 |
1 files changed, 129 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 700dec4..0a131f5 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -48,6 +48,7 @@ #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) #:use-module (gnu packages ghostscript) + #:use-module (gnu packages graph) #:use-module (gnu packages gtk) #:use-module (gnu packages guile) #:use-module (gnu packages image) @@ -61,6 +62,7 @@ #:use-module (gnu packages mpi) #:use-module (gnu packages ncurses) #:use-module (gnu packages ocaml) + #:use-module (gnu packages parallel) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages protobuf) @@ -2483,6 +2485,133 @@ multiple sequence alignment.") license:zlib ; deps/sonLib/externalTools/cutest license:boost1.0)))) ; catch.hpp +(define-public pggb + (let ((commit "9ebff27320382e470ed38a85b4448402e1e7c353") + (revision "1")) + (package + (name "pggb") + (version (git-version "0.5.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pangenome/pggb") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0rgpj52q3ai7f1saqbilgx5gz4f403x3427wq649qwv84ivmi1sf")))) + (build-system copy-build-system) + (arguments + (list + #:install-plan + #~'(("pggb" "bin/") + ("partition-before-pggb" "bin/") + ("scripts/" "bin/") + ("scripts" "bin/scripts")) + #:phases + #~(modify-phases %standard-phases + (add-before 'install 'patch-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "scripts/vcf_preprocess.sh" + (("bcftools ") + (string-append (search-input-file inputs "/bin/bcftools") " "))) + (wrap-script "scripts/net2communities.py" + `("GUIX_PYTHONPATH" ":" prefix + (,(getenv "GUIX_PYTHONPATH")))))) + (add-after 'install 'wrap-scripts + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (for-each + (lambda (file) + (wrap-script file + `("PATH" ":" prefix + ,(map (lambda (input) (string-append input "/bin")) + '#$(map (lambda (label) (this-package-input label)) + (list "bcftools" + "bedtools" + "gfaffix" + "fastix" + "multiqc" + "mummer" + "odgi-hwcaps" + "pafplot" + "parallel" + "pigz" + "r-data-table" + "rtg-tools" + "samtools" + "seqwish" + "smoothxg" + ;"tabix" + "vcfbub" + "vcflib" + "vg" + "wfmash-hwcaps")))))) + (list (string-append out "/bin/pggb") + (string-append out "/bin/partition-before-pggb") + (string-append out "/bin/gfa2evaluation.sh") + (string-append out "/bin/scripts/gfa2evaluation.sh")))))) + (add-after 'install 'substitute-file-paths + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (substitute* (string-append out "/bin/gfa2evaluation.sh") + (("/usr/local/bin/vcf_preprocess.sh") + (string-append out "/bin/vcf_preprocess.sh")) + (("/usr/local/bin/nucmer2vcf.R") + (string-append out "/bin/nucmer2vcf.R"))))))))) + (inputs + (list bcftools + bedtools + gfaffix + guile-3.0 ; for wrap-script + fastix + multiqc + mummer + odgi-hwcaps + pafplot + parallel + pigz + python-igraph + python-pycairo + python-wrapper + r-data-table + rtg-tools + samtools + seqwish + smoothxg + ;tabix + vcfbub + vcflib + vg + wfmash-hwcaps)) + (home-page "https://doi.org/10.1101/2023.04.05.535718") + (synopsis "PanGenome Graph Builder") + (description "@command{pggb} builds +@url{https://doi.org/10.1146%2Fannurev-genom-120219-080406, pangenome} +@url{https://doi.org/10.1038/nbt.4227, variation graphs} from a set of input +sequences. +A pangenome variation graph is a kind of generic multiple sequence alignment. +It lets us understand any kind of sequence variation between a collection of +genomes. It shows us similarity where genomes walk through the same parts of +the graph, and differences where they do not. +@command{pggb} generates this kind of graph using an all-to-all alignment of +input sequences (@url{https://github.com/waveygang/wfmash, wfmash}), graph +induction (@url{https://doi.org/10.1101/2022.02.14.480413, seqwish}), and +progressive normalization (@url{https://github.com/pangenome/smoothxg, +smoothxg}, @url{https://github.com/marschall-lab/GFAffix, gfaffix}). After +construction, @command{pggb} generates diagnostic visualizations of the graph +(@url{https://doi.org/10.1093/bioinformatics/btac308, odgi}). A variant call +report (in VCF) representing both small and large variants can be generated +based on any reference genome included in the graph +(@url{https://github.com/vgteam/vg, vg}). @command{pggb} writes its output in +@url{https://github.com/GFA-spec/GFA-spec/blob/master/GFA1.md, GFAv1} format, +which can be used as input by numerous \"genome graph\" and pangenome tools, +such as the @url{https://github.com/vgteam/vg, vg} and +@url{https://doi.org/10.1093/bioinformatics/btac308, odgi} toolkits. +@command{pggb} has been tested at scale in the @acronym{Human Pangenome +Reference Consortium, HPRC} as a method to build a graph from the +@url{https://doi.org/10.1101/2022.07.09.499321, draft human pangenome}.") + (license license:expat)))) + (define-public ucsc-genome-browser (package (name "ucsc-genome-browser") |