diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 256 |
1 files changed, 199 insertions, 57 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5f4a6ab7ac..8a00420946 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4,8 +4,8 @@ ;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2016, 2020, 2021 Roel Janssen <roel@gnu.org> -;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il> -;;; Copyright © 2016, 2020 Marius Bakke <mbakke@fastmail.com> +;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021, 2022 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2016, 2020, 2022 Marius Bakke <marius@gnu.org> ;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com> ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017, 2021 Arun Isaac <arunisaac@systemreboot.net> @@ -2218,7 +2218,7 @@ well as many of the command line options.") (define-public bwa-meth (package (name "bwa-meth") - (version "0.2.2") + (version "0.2.3") (source (origin (method git-fetch) (uri (git-reference @@ -2227,7 +2227,7 @@ well as many of the command line options.") (file-name (git-file-name name version)) (sha256 (base32 - "17j31i7zws5j7mhsq9x3qgkxly6mlmrgwhfq0qbflgxrmx04yaiz")))) + "0c695lkrr0996zwkibl7324wg2vxmn6522sz30xv4a9gaf0lnbh3")))) (build-system python-build-system) (arguments `(#:phases @@ -2238,8 +2238,7 @@ well as many of the command line options.") (("bwa (mem|index)" _ command) (string-append (which "bwa") " " command)) ;; There's an ill-advised check for "samtools" on PATH. - (("^checkX.*") "")) - #t))))) + (("^checkX.*") ""))))))) (inputs (list bwa)) (native-inputs @@ -3340,8 +3339,8 @@ data and settings.") texlive-hyperref texlive-ms texlive-latex-natbib - texlive-bibtex ; style files used by natbib - texlive-pgf ; tikz + texlive-bibtex ;style files used by natbib + texlive-pgf ;tikz texlive-latex-verbatimbox))) ("imagemagick" ,imagemagick))) (home-page "https://dorina.mdc-berlin.de/public/rajewsky/discrover/") @@ -10895,6 +10894,9 @@ once. This package provides tools to perform Drop-seq analyses.") (add-before 'bootstrap 'autoreconf (lambda _ (invoke "autoreconf" "-vif"))) + (add-before 'configure 'set-PYTHONPATH + (lambda _ + (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH")))) (add-before 'check 'set-timezone ;; The readr package is picky about timezones. (lambda* (#:key inputs #:allow-other-keys) @@ -10969,7 +10971,10 @@ expression report comparing samples in an easily configurable manner.") (modify-phases %standard-phases (add-before 'bootstrap 'autoreconf (lambda _ - (invoke "autoreconf" "-vif")))))) + (invoke "autoreconf" "-vif"))) + (add-before 'configure 'set-PYTHONPATH + (lambda _ + (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))))) (inputs (list grep coreutils @@ -11055,6 +11060,9 @@ in an easily configurable manner.") (add-before 'bootstrap 'autoreconf (lambda _ (invoke "autoreconf" "-vif"))) + (add-before 'configure 'set-PYTHONPATH + (lambda _ + (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH")))) (add-before 'check 'set-timezone ;; The readr package is picky about timezones. (lambda* (#:key inputs #:allow-other-keys) @@ -11123,7 +11131,10 @@ methylation and segmentation.") (modify-phases %standard-phases (add-before 'bootstrap 'autoreconf (lambda _ - (invoke "autoreconf" "-vif")))))) + (invoke "autoreconf" "-vif"))) + (add-before 'configure 'set-PYTHONPATH + (lambda _ + (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))))) (native-inputs (list automake autoconf)) (inputs @@ -11197,7 +11208,10 @@ based methods.") (modify-phases %standard-phases (add-before 'bootstrap 'autoreconf (lambda _ - (invoke "autoreconf" "-vif")))))) + (invoke "autoreconf" "-vif"))) + (add-before 'configure 'set-PYTHONPATH + (lambda _ + (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))))) (native-inputs (list automake autoconf)) (inputs @@ -11395,7 +11409,7 @@ version does count multisplits.") (define-public minimap2 (package (name "minimap2") - (version "2.23") + (version "2.24") (source (origin (method url-fetch) @@ -11404,7 +11418,7 @@ version does count multisplits.") "minimap2-" version ".tar.bz2")) (sha256 (base32 - "00ngbz1swcgxk5apx9dz5xkh1z8abdpysx5lc7w8fbrfxp41w0j0")))) + "05d6h2c1h95s5vblf1fijn9g0r4g69nsvkabji42j642y0gw7m4x")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; there are none @@ -11681,6 +11695,49 @@ including: ;; the GPL, but the license headers include the "or later" clause. (license license:gpl3+))) +(define-public r-dyngen + (let ((commit "37fd1798fcbd41093fb3d7775bb2d268e2fc82b6") + (revision "1")) + (package + (name "r-dyngen") + (version (git-version "1.0.3" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dynverse/dyngen") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "05pr6v1b8yji1jnj3fwx0crmg8ay6yy6lp9qjmcyvhkwbmf3kvc7")))) + (properties `((upstream-name . "dyngen"))) + (build-system r-build-system) + (propagated-inputs + (list r-assertthat + r-dplyr + r-dynutils + r-ggplot2 + r-ggraph + r-ggrepel + r-gillespiessa2 + r-igraph + r-lmds + r-matrix + r-patchwork + r-pbapply + r-purrr + r-rlang + r-tibble + r-tidygraph + r-tidyr + r-viridis)) + (home-page "https://github.com/dynverse/dyngen") + (synopsis "Multi-Modal simulator for single-cell omics analyses") + (description + "This package provides a multi-modal simulation engine for studying +dynamic cellular processes at single-cell resolution.") + (license license:expat)))) + (define-public r-circus (package (name "r-circus") @@ -12013,7 +12070,7 @@ implementation differs in these ways: python-igraph python-joblib python-legacy-api-wrap - python-louvain-0.6 + python-louvain-0.7 python-matplotlib python-natsort python-networkx @@ -13826,6 +13883,35 @@ vast-tools, an RNA-Seq pipeline for alternative splicing analysis. The plots are generated using @code{ggplot2}.") (license license:expat))) +(define-public r-scopeloomr + (let ((commit "99726f5f7da794042036b73924b6a10d6e7b4d5d") + (revision "1")) + (package + (name "r-scopeloomr") + (version (git-version "0.13.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/aertslab/SCopeLoomR") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1ci17ms0c0hf7yfp9ckcg7a2y1s0nm19jj3cifsd55hwc0gdglmz")))) + (properties `((upstream-name . "SCopeLoomR"))) + (build-system r-build-system) + (propagated-inputs + (list r-base64enc r-hdf5r r-igraph r-matrix r-plyr r-rjson r-rlist)) + (home-page "https://github.com/aertslab/SCopeLoomR") + (synopsis "Build .loom files and extract data from them") + (description + "This is an R package to build generic @code{.loom} files aligning with +the default naming convention of the @code{.loom} format and to integrate +other data types e.g.: regulons (SCENIC), clusters from Seurat, trajectory +information... The package can also be used to extract data from @code{.loom} +files.") + (license license:expat)))) + (define-public vbz-compression (package (name "vbz-compression") @@ -14606,55 +14692,48 @@ alignments, trees and genomic annotations.") (license license:bsd-3))) (define-public python-gffutils - ;; The latest release is older more than a year than the latest commit - (let ((commit "4034c54600813b1402945e12faa91b3a53162cf1") - (revision "1")) - (package - (name "python-gffutils") - (version (git-version "0.9" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/daler/gffutils") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1rwafjdnbir5wnk0ap06ww4lra3p5frhy7mfs03rlldgfnwxymsn")))) - (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda _ + (package + (name "python-gffutils") + (version "0.10.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/daler/gffutils") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1gkzk7ps6w3ai2r81js9s9bzpba0jmxychnd2da6n9ggdnf2xzqz")))) + (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? ;; Tests need to access the HOME directory (setenv "HOME" "/tmp") - (invoke "nosetests" "-a" "!slow"))) - (add-after 'unpack 'make-gz-files-writable - (lambda _ - (for-each make-file-writable - (find-files "." "\\.gz")) - #t))))) - (propagated-inputs - (list python-argcomplete - python-argh - python-biopython - python-pybedtools - python-pyfaidx - python-simplejson - python-six)) - (native-inputs - (list python-nose)) - (home-page "https://github.com/daler/gffutils") - (synopsis "Tool for manipulation of GFF and GTF files") - (description - "python-gffutils is a Python package for working with and manipulating + (invoke "nosetests" "-a" "!slow"))))))) + (propagated-inputs + (list python-argcomplete + python-argh + python-biopython + python-pybedtools + python-pyfaidx + python-simplejson + python-six)) + (native-inputs + (list python-nose)) + (home-page "https://github.com/daler/gffutils") + (synopsis "Tool for manipulation of GFF and GTF files") + (description + "python-gffutils is a Python package for working with and manipulating the GFF and GTF format files typically used for genomic annotations. The files are loaded into a SQLite database, allowing much more complex manipulation of hierarchical features (e.g., genes, transcripts, and exons) than is possible with plain-text methods alone.") - (license license:expat)))) + (license license:expat))) (define-public indelfixer (package @@ -15568,6 +15647,69 @@ aligner.") ;; bwa itself is licenced under GNU General Public License v3.0. (license license:mpl2.0))) +(define-public scvelo + (package + (name "scvelo") + (version "0.2.4") + (source + (origin + (method url-fetch) + (uri (pypi-uri "scvelo" version)) + (sha256 + (base32 "0h5ha1459ljs0qgpnlfsw592i8dxqn6p9bl08l1ikpwk36baxb7z")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; Numba needs a writable dir to cache functions. + (add-before 'check 'set-numba-cache-dir + (lambda _ + (setenv "NUMBA_CACHE_DIR" "/tmp"))) + (replace 'check + (lambda* (#:key outputs tests? #:allow-other-keys) + (when tests? + ;; The discovered test file names must match the names of the + ;; compiled files, so we cannot run the tests from + ;; /tmp/guix-build-*. + (with-directory-excursion + (string-append (assoc-ref outputs "out") + "/lib/python3.9/site-packages/scvelo/core/tests/") + (invoke "pytest" "-v")))))))) + (propagated-inputs + (list python-anndata + python-hnswlib + python-isort + python-igraph + python-loompy + python-louvain + python-matplotlib + python-numba + python-numpy + python-pandas + python-scanpy + python-scikit-learn + python-scipy + python-umap-learn + pybind11)) + (native-inputs + (list python-black + python-flake8 + python-hypothesis + python-pre-commit + python-pytest + python-setuptools-scm + python-wheel)) + (home-page "https://scvelo.org") + (synopsis "RNA velocity generalized through dynamical modeling") + (description "ScVelo is a scalable toolkit for RNA velocity analysis in +single cells. RNA velocity enables the recovery of directed dynamic +information by leveraging splicing kinetics. scVelo generalizes the concept of +RNA velocity by relaxing previously made assumptions with a stochastic and a +dynamical model that solves the full transcriptional dynamics. It thereby +adapts RNA velocity to widely varying specifications such as non-stationary +populations.") + (license license:bsd-3))) + (define-public scregseg (package (name "scregseg") |