diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 74 |
1 files changed, 63 insertions, 11 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cb0bdf766e..508f5ea09a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -93,6 +93,7 @@ #:use-module (gnu packages gcc) #:use-module (gnu packages gd) #:use-module (gnu packages golang) + #:use-module (gnu packages golang-check) #:use-module (gnu packages glib) #:use-module (gnu packages graph) #:use-module (gnu packages graphics) @@ -4695,26 +4696,16 @@ accurately delineate genomic rearrangements throughout the genome.") (arguments (list #:install-source? #false ;fails - #:tests? #false ;"cargo test" ignores build.rs #:phases #~(modify-phases %standard-phases (add-after 'unpack 'prepare-test-files (lambda _ (delete-file "Cargo.lock") - (substitute* "liftover-rs/Cargo.toml" - (("anyhow = \"1\"") "anyhow = \"1.0.65\"")) (substitute* "liftover-rs/prepare-test.sh" (("/bin/bash") (string-append #$(this-package-native-input "bash") "/bin/bash"))) (invoke "bash" "prepare-test-files.sh"))) - (add-before 'patch-cargo-checksums 'do-not-build-xz - (lambda _ - ;; Detection of liblzma (in rust-lzma-sys, pulled in by - ;; rust-hts-sys) doesn't seem to work, or perhaps it really does - ;; request a static build somewhere. - (substitute* "guix-vendor/rust-lzma-sys-0.1.17.tar.xz/build.rs" - (("if .want_static && .msvc && pkg_config::probe_library\\(\"liblzma\"\\).is_ok\\(\\)") "")))) (add-before 'install 'chdir (lambda _ (chdir "transanno")))) #:cargo-inputs @@ -4736,7 +4727,8 @@ accurately delineate genomic rearrangements throughout the genome.") #:cargo-development-inputs `(("rust-clap" ,rust-clap-2) ("rust-lazy-static" ,rust-lazy-static-1)))) - (native-inputs (list bash)) + (native-inputs (list bash pkg-config)) + (inputs (list xz)) (home-page "https://github.com/informationsea/transanno") (synopsis "LiftOver tool for new genome assemblies") (description "This package provides an accurate VCF/GFF3/GTF LiftOver tool @@ -10285,6 +10277,66 @@ figures. This tool will create clean markdown reports about what you just discovered.") (license license:gpl3)))) +(define-public r-metacell + (let ((commit "d6a6926d103ee0cb34a611c753572429c94a53d9") + (revision "1")) + (package + (name "r-metacell") + (version (git-version "0.3.41" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tanaylab/metacell/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0zrsckr3y35x37mj3ibm6scyqx925s84wzrz1i42fnm9n3msc265")))) + (properties `((upstream-name . "metacell"))) + (build-system r-build-system) + (propagated-inputs (list r-cluster + r-cowplot + r-data-table + r-dbscan + r-domc + r-dplyr + r-entropy + r-ggplot2 + r-graph + r-igraph + r-kernsmooth + r-magrittr + r-matrix + r-matrixstats + r-pdist + r-pheatmap + r-plyr + r-rcolorbrewer + r-rcurl + r-rgraphviz + r-slam + r-singlecellexperiment + r-svglite + r-tgconfig + r-tgstat + r-tgutil + r-tidyr + r-umap + r-umap + r-zoo)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/tanaylab/metacell/") + (synopsis "Meta cell analysis for single cell RNA-seq data") + (description + "This package facilitates the analysis of single-cell RNA-seq UMI matrices. +It does this by computing partitions of a cell similarity graph into +small homogeneous groups of cells, which are defined as metacells (MCs). +The derived MCs are then used for building different representations of +the data, allowing matrix or 2D graph visualization forming a basis for +analysis of cell types, subtypes, transcriptional gradients,cell-cycle +variation, gene modules and their regulatory models and more.") + (license license:expat)))) + (define-public r-snapatac (package (name "r-snapatac") |