diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 595 |
1 files changed, 554 insertions, 41 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6e909773a7..055c8ca47b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2014-2023 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> @@ -11,7 +11,7 @@ ;;; Copyright © 2017, 2021, 2022 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com> -;;; Copyright © 2018, 2019, 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> +;;; Copyright © 2018-2023 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; Copyright © 2019, 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com> ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org> @@ -21,9 +21,9 @@ ;;; Copyright © 2020 Bonface Munyoki Kilyungi <bonfacemunyoki@gmail.com> ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com> ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de> -;;; Copyright © 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com> +;;; Copyright © 2021, 2022, 2023 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2021 Felix Gruber <felgru@posteo.net> -;;; Copyright © 2022 Navid Afkhami <navid.afkhami@mdc-berlin.de> +;;; Copyright © 2022, 2023 Navid Afkhami <navid.afkhami@mdc-berlin.de> ;;; Copyright © 2022 Antero Mejr <antero@mailbox.org> ;;; ;;; This file is part of GNU Guix. @@ -512,6 +512,106 @@ BED, GFF/GTF, VCF.") (inputs (list samtools zlib)))) +(define-public bitmapperbs + (package + (name "bitmapperbs") + (version "1.0.2.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/chhylp123/BitMapperBS/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "02ksssfnvmpskld0a2016smfz5nrzm3d90v8974f3cpzywckvp8v")) + (modules '((guix build utils))) + ;; This package bundles a modified copy of htslib, so we cannot + ;; unbundle it. + (snippet + '(begin + (delete-file-recursively "libdivsufsort-2.0.1") + (delete-file-recursively "pSAscan-0.1.0"))))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #false + #:make-flags '(list "bitmapperBS") + ;; The build system checks for CPU features. For this reason, we want + ;; users to build it locally instead of using substitutes. + #:substitutable? #false + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-build-system + (lambda _ + (substitute* "Makefile" + (("make prefix=../htslib_aim install") + (string-append "make prefix=" #$output " install-so")) + (("htslib_aim/include") "htslib") + (("htslib_aim/lib") + (string-append #$output "/lib"))))) + (add-after 'unpack 'patch-references-to-psascan + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "Makefile" + (("\"(./)?psascan" pre all) + (string-append "\"" pre (search-input-file inputs "/bin/psascan")))))) + (delete 'configure) + (replace 'install + (lambda _ + (install-file "bitmapperBS" + (string-append #$output "/bin/"))))))) + (inputs + (list libdivsufsort psascan zlib)) + (home-page "https://github.com/chhylp123/BitMapperBS/") + (synopsis "Read aligner for whole-genome bisulfite sequencing") + (description + "BitMapperBS is memory-efficient aligner that is designed for +whole-genome bisulfite sequencing (WGBS) reads from directional protocol.") + (license license:asl2.0))) + +(define-public cellsnp-lite + ;; Last release is from November 2021 and does not contain fixes. + (let ((commit "0885d746b0b1ea65c8ef92f8943ca7669ca9734a") + (revision "0")) + (package + (name "cellsnp-lite") + (version (git-version "1.2.2" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/single-cell-genetics/cellsnp-lite") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1qrvqgbvw6mbhpyqvqbmvv8dmyc67bsk1041cn7ib6zmd47qm444")))) + (build-system gnu-build-system) + (arguments + (list + #:configure-flags + #~(list (string-append "--with-htslib=" + #$(this-package-input "htslib"))))) + (inputs + (list curl + htslib + openssl + zlib)) + (native-inputs + (list autoconf)) + (home-page "https://cellsnp-lite.readthedocs.io") + (synopsis "Pileup expresses alleles in single-cell or bulk RNA-seq data") + (description + "This package is designed to pileup the expressed alleles in +single-cell or bulk RNA-seq data, which can be directly used for donor +deconvolution in multiplexed single-cell RNA-seq data, particularly with other +packages, which assigns cells to donors and detects doublets as vireo, even +without genotyping reference. + +This package is the C version of the deprecated cellSNP implemented in Python. +Compared to cellSNP, this package is more efficient with higher speed and less +memory usage.") + (license license:asl2.0)))) + (define-public pbcopper (package (name "pbcopper") @@ -647,6 +747,41 @@ high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib.") (license license:lgpl2.0+)))) +(define-public r-streamgraph + (let ((commit "76f7173ec89d456ace5943a512e20b1f6810bbcb") + (revision "1")) + (package + (name "r-streamgraph") + (version (git-version "0.9.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hrbrmstr/streamgraph") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "010rhnby5a9dg08jvlkr65b3p9iipdxi2f5m1k6j53s80p25yvig")))) + (properties `((upstream-name . "streamgraph"))) + (build-system r-build-system) + (propagated-inputs + (list r-dplyr + r-htmltools + r-htmlwidgets + r-magrittr + r-tidyr + r-xts)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/hrbrmstr/streamgraph") + (synopsis "Htmlwidget for building streamgraph visualizations") + (description + "A streamgraph is a type of stacked area chart. It represents the +evolution of a numeric variable for several groups. Areas are usually +displayed around a central axis, and edges are rounded to give a flowing +shape. This package provides an @code{htmlwidget} for building streamgraph +visualizations.") + (license license:expat)))) + (define-public pbbam (package (name "pbbam") @@ -933,6 +1068,13 @@ intended to behave exactly the same as the original BWK awk.") Format (GFF) with Biopython integration.") (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE")))) +(define-public python-bcbio-gff/biopython-1.73 + (package + (inherit python-bcbio-gff) + (propagated-inputs + (modify-inputs (package-propagated-inputs python-bcbio-gff) + (replace "python-biopython" python-biopython-1.73))))) + (define-public python-cellbender (package (name "python-cellbender") @@ -946,7 +1088,7 @@ Format (GFF) with Biopython integration.") (file-name (git-file-name name version)) (sha256 (base32 - "12q22va7rbc3sx9ygc6p6hh6xw9wbqjmhba5h5gb836p5xplj5fa")))) + "0h9d9pznffdbya631hkk7b7jwjrgx5saqssar1d42qbyvdji3hgy")))) (build-system pyproject-build-system) (arguments (list #:tests? #false)) ;there are none @@ -971,6 +1113,95 @@ Format (GFF) with Biopython integration.") from high-throughput single-cell RNA sequencing (scRNA-seq) data.") (license license:bsd-3))) +(define-public python-cmseq + (package + (name "python-cmseq") + (version "1.0.4") + (source (origin + (method url-fetch) + (uri (pypi-uri "CMSeq" version)) + (sha256 + (base32 + "0p6a99c299m5wi2z57dgqz52m1z3nfr8mv7kdnk2jvl2p9nql0wk")))) + (build-system pyproject-build-system) + (arguments + (list + #:tests? #false ;there are no tests + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'patch-samtools-reference + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "cmseq/cmseq.py" + (("'samtools'") + (string-append "'" (search-input-file inputs "/bin/samtools") "'")))))))) + (inputs (list samtools)) + (propagated-inputs + (list python-bcbio-gff/biopython-1.73 + python-biopython-1.73 + python-numpy + python-pandas + python-pysam + python-scipy)) + (home-page "https://github.com/SegataLab/cmseq/") + (synopsis "Set of utilities on sequences and BAM files") + (description + "CMSeq is a set of commands to provide an interface to .bam files for coverage +and sequence consensus.") + (license license:expat))) + +(define-public python-demuxem + (package + (name "python-demuxem") + (version "0.1.7") + (source (origin + (method url-fetch) + (uri (pypi-uri "demuxEM" version)) + (sha256 + (base32 + "1bhyxqjk44bmyd26m1smapf68wyf7252kk65i27k50dd3kswgnd6")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-docopt + python-importlib-metadata + python-numpy + python-pandas + python-pegasusio + python-scikit-learn + python-scipy + python-seaborn)) + (native-inputs (list python-cython python-setuptools-scm)) + (home-page "https://github.com/lilab-bcb/demuxEM") + (synopsis "Analyze cell-hashing/nucleus-hashing data") + (description + "This is a Python module for analyzing cell-hashing/nucleus-hashing data. +It is the demultiplexing module of Pegasus, which is used by Cumulus in the +demultiplexing step.") + (license license:bsd-3))) + +(define-public python-hclust2 + (package + (name "python-hclust2") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "hclust2" version)) + (sha256 + (base32 + "0v89n2g42d7jhgfs8glf06apgxx6aswp3mfisgnhm518cv8z2rwn")))) + (build-system pyproject-build-system) + (arguments (list #:tests? #f)) ;there are no tests + (propagated-inputs + (list python-matplotlib + python-numpy + python-pandas + python-scipy)) + (home-page "https://github.com/SegataLab/hclust2/") + (synopsis "Plotting heat-maps for publications") + (description + "Hclust2 is a handy tool for plotting heat-maps with several useful options +to produce high quality figures that can be used in publications.") + (license license:expat))) + (define-public python-htsget (package (name "python-htsget") @@ -993,6 +1224,74 @@ protocol. It provides a simple and reliable way to retrieve genomic data from servers supporting the protocol.") (license license:asl2.0))) +(define-public python-pegasusio + (package + (name "python-pegasusio") + (version "0.7.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "pegasusio" version)) + (sha256 + (base32 + "0gqygspdy398vjymdy6756jmk99s7fhwav9rivdx59kpqjcdxaz9")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-anndata + python-docopt + python-h5py + python-importlib-metadata + python-loompy + python-natsort + python-numpy + python-pandas + python-pillow + python-scipy + python-zarr)) + (native-inputs (list python-cython python-setuptools-scm)) + (home-page "https://github.com/lilab-bcb/pegasusio") + (synopsis "Read or write single-cell genomics data") + (description + "Pegasusio is a Python package for reading or writing single-cell +genomics data.") + (license license:bsd-3))) + +(define-public python-phylophlan + (package + (name "python-phylophlan") + (version "3.0.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/biobakery/phylophlan") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1wz70xzxqx2sf5flmf45m15jq027dqijfaj1r51pl50w5x6dkawx")))) + (build-system pyproject-build-system) + (arguments (list #:tests? #f)) ;there are no tests + (propagated-inputs + (list python-biopython + python-dendropy + python-matplotlib + python-numpy + python-pandas + python-seaborn)) + (home-page "https://github.com/biobakery/phylophlan") + (synopsis + "Phylogenetic analysis of microbial isolates and genomes from metagenomes") + (description + "This package is an integrated pipeline for large-scale phylogenetic +profiling of genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and +easy-to-use method for large-scale microbial genome characterization and +phylogenetic analysis at multiple levels of resolution. This software package +can assign both genomes and @acronym{MAGs, metagenome-assembled genomes} to +@acronym{SGBs, species-level genome bins}. PhyloPhlAn can reconstruct +strain-level phylogenies using clade- specific maximally informative +phylogenetic markers, and can also scale to very large phylogenies comprising +>17,000 microbial species.") + (license license:expat))) + (define-public python-pybedtools (package (name "python-pybedtools") @@ -6865,6 +7164,38 @@ Values such as sequence name, sequence description, sequence quality and the sequence itself can be retrieved from these databases.") (license license:bsd-3))) +(define-public python-slamdunk + (package + (name "python-slamdunk") + (version "0.4.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/t-neumann/slamdunk") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0lv3h5k2pn1pz35kz0wk5xmricxzy8qscs2y7nwh0k6x4pn0m0s5")))) + (build-system python-build-system) + (propagated-inputs + (list python-biopython + python-intervaltree + python-joblib + python-pandas + python-pybedtools + python-pysam)) + (native-inputs + (list python-cython python-pytest)) + (home-page "https://t-neumann.github.io/slamdunk/") + (synopsis "Streamline SLAM-seq analysis with high sensitivity") + (description "SlamDunk is a fully automated tool for automated, robust, +scalable and reproducible SLAMseq data analysis. Diagnostic plotting features +and a MultiQC plugin will make your SLAMseq data ready for immediate QA and +interpretation.") + (license license:agpl3+))) + (define-public python-taggd (package (name "python-taggd") @@ -7721,6 +8052,36 @@ sequence.") 3D perspective axes, 3D perspective annotations, and wireframe plots.") (license license:gpl3+)))) +(define-public r-ggsankey + (let ((commit "be08dd0f86eaee9f9ff9e7ff95d47930660a3c36") + (revision "1")) + (package + (name "r-ggsankey") + (version (git-version "0.0.99999" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/davidsjoberg/ggsankey") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0acpmydqqc91pq5p9wpkpmgqp3nhiljabd7d3i00kwhjxgm2bvba")))) + (properties `((upstream-name . "ggsankey"))) + (build-system r-build-system) + (propagated-inputs (list r-dplyr + r-ggplot2 + r-magrittr + r-purrr + r-stringr + r-tidyr)) + (home-page "https://github.com/davidsjoberg/ggsankey") + (synopsis "Sankey, Alluvial and Sankey bump plots") + (description + "This package provides a package that makes it easy to implement +sankey, alluvial and sankey bump plots in @code{ggplot2}.") + (license license:expat)))) + (define-public r-gutils (let ((commit "10e36c7b580aacb2d952140a3fdd82418aaddea6") (revision "1")) @@ -7943,6 +8304,93 @@ tasks.") Pore-C concatemers.") (license license:gpl3)))) +(define-public r-doubletcollection + (let ((commit "c0d62f1853942ee6a087eaf7b000d9e4261e2dfd") + (revision "1")) + (package + (name "r-doubletcollection") + (version (git-version "1.1.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/xnnba1984/DoubletCollection") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "02cvibyc2nwc4037ramm5cskjwyrb9ib9hkrfhmvhbslkn5ixz1v")))) + (properties `((upstream-name . "DoubletCollection"))) + (build-system r-build-system) + (propagated-inputs (list r-biocgenerics + r-doubletfinder + r-gam + r-ggplot2 + r-ggthemes + r-mast + r-mclust + r-prroc + r-reticulate + r-scales + r-scdblfinder + r-scds + r-seurat + r-singlecellexperiment + r-slingshot + r-summarizedexperiment)) + (home-page "https://github.com/xnnba1984/DoubletCollection") + (synopsis "Tool for finding doublets in scRNA-seq data") + (description + "This is an R package that integrates the installation of +doublet-detection methods. In addition, this tool is used for execution and +benchmark of those eight mentioned methods.") + (license license:gpl3+)))) + +(define-public r-psupertime + (let ((commit "73825a28d3bd9bc881c15ee0c4c218eec1c9c207") + (revision "1")) + (package + (name "r-psupertime") + (version (git-version "0.2.6" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/wmacnair/psupertime") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "00h1r3ffz6m9dwcgkvyki8405b059qn6mnjsd8d76a1rabaf2vfh")))) + (properties `((upstream-name . "psupertime"))) + (build-system r-build-system) + (propagated-inputs + (list r-cowplot + r-data-table + r-fastcluster + r-forcats + r-ggplot2 + r-glmnet + r-knitr + r-matrix + r-rcolorbrewer + r-scales + r-scran + r-singlecellexperiment + r-stringr + r-summarizedexperiment + r-topgo)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/wmacnair/psupertime") + (synopsis + "Psupertime is supervised pseudotime for single cell RNAseq data") + (description + "Psupertime is supervised pseudotime for single cell RNAseq data. It +uses single cell RNAseq data, where the cells have a known ordering. This +ordering helps to identify a small number of genes which place cells in that +known order. It can be used for discovery of relevant genes, for +identification of subpopulations, and characterization of further unknown or +differently labelled data.") + (license license:gpl3)))) + (define-public r-pando (package (name "r-pando") @@ -8132,6 +8580,38 @@ clustering analysis, differential analysis, motif inference and exploration of single cell ATAC-seq sequencing data.") (license license:gpl3))) +(define-public r-tsis + (let ((commit "24460298fbe1d26e4da390f6e4f3d4d9d62334dc") + (revision "1")) + (package + (name "r-tsis") + (version (git-version "0.2.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/wyguo/TSIS") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "17c8i25iwhldvs3c51m0wny40iffm8szzijalpwrxhzbv0xa94rb")))) + (properties `((upstream-name . "TSIS"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://github.com/wyguo/TSIS") + (synopsis "Time-series isoform switch of alternative splicing") + (description + "TSIS is used for detecting transcript isoform switches in time-series +data. Transcript isoform switches occur when a pair of alternatively spliced +isoforms reverse the order of their relative expression levels. TSIS +characterizes the transcript switch by defining the isoform switch time-points +for any pair of transcript isoforms within a gene. In addition, this tool +describes the switch using five different features or metrics. Also it +filters the results with user’s specifications and visualizes the results +using different plots for the user to examine further details of the +switches.") + (license license:gpl3)))) + (define-public r-umi4cpackage (let ((commit "88b07d896a137418ba6c31c2474b9dbe1d86fc20") (revision "1")) @@ -16689,20 +17169,20 @@ translates between different variant encodings.") (license license:asl2.0)))) (define-public r-signac - (let ((commit "458e647b503c3472b0b98c0aeca934f452e039ee") - (revision "2")) + (let ((commit "af4142724b72574d957f7fe3d422ed5828ec3ad0") + (revision "1")) (package (name "r-signac") - (version (git-version "1.6.0" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/timoast/signac/") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "1hgwpgighkvfkai80n4d2252s4sdpa4faag4ncdiylicl5wa7lbj")))) + (version (git-version "1.9.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/timoast/signac/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ps0lp1dcy20r6lakil6ih81m04r0s6fnirvfjf01sfs0gsyddww")))) (properties `((upstream-name . "Signac"))) (build-system r-build-system) (inputs (list zlib)) @@ -16715,27 +17195,22 @@ translates between different variant encodings.") r-future-apply r-genomeinfodb r-genomicranges - r-ggforce r-ggplot2 - r-ggrepel - r-ggseqlogo r-iranges r-irlba - r-lsa r-matrix r-patchwork r-pbapply - r-qlcmatrix r-rcpp r-rcpproll r-rsamtools r-s4vectors r-scales - r-seurat r-seuratobject r-stringi r-tidyr - r-tidyselect)) + r-tidyselect + r-vctrs)) (home-page "https://github.com/timoast/signac/") (synopsis "Analysis of single-cell chromatin data") (description @@ -17503,21 +17978,20 @@ Genomics with R\".") (license license:gpl3)))) (define-public r-cytonorm - (let ((commit "e4b9d343ee65db3c422800f1db3e77c25abde987") + (let ((commit "166f9ff3d692278241018c2846cb4f86ab16065b") (revision "1")) (package (name "r-cytonorm") - (version (git-version "0.0.7" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/saeyslab/CytoNorm") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0h2rdy15i4zymd4dv60n5w0frbsdbmzpv99dgm0l2dn041qv7fah")))) + (version (git-version "0.0.10" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/saeyslab/CytoNorm") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0vbqy3b26j1zqmwgqx59kkn9pm2m0qwlcppskvahrxcwrj6m1s5y")))) (properties `((upstream-name . "CytoNorm"))) (build-system r-build-system) (propagated-inputs @@ -17567,6 +18041,28 @@ interest.") ;; Any version of the GPL (license license:gpl3+)))) +(define-public python-vireosnp + (package + (name "python-vireosnp") + (version "0.5.7") + (source (origin + (method url-fetch) + (uri (pypi-uri "vireoSNP" version)) + (sha256 + (base32 + "02ybhzivsxwnb1axlgbs63wni1j27xajnkl4jw1ps5vmsz2l4b0d")))) + (build-system python-build-system) + (propagated-inputs (list python-matplotlib python-numpy python-scipy)) + (home-page "https://github.com/huangyh09/vireoSNP") + (synopsis "Deconvolution based on SNP for multiplexed scRNA-seq data") + (description + "This package provides a deconvolution based on Single Nucleotide +Position (SNP) for multiplexed scRNA-seq data. The name vireo stand for +Variational Inference for Reconstructing Ensemble Origin by expressed SNPs in +multiplexed scRNA-seq data and follows the clone identification from +single-cell data named @url{https://github.com/PMBio/cardelino, cardelino}.") + (license license:asl2.0))) + (define-public ccwl (package (name "ccwl") @@ -17804,7 +18300,7 @@ module capable of computing base-level alignments for very large sequences.") (define-public gdcm (package (name "gdcm") - (version "2.8.9") + (version "3.0.20") (source (origin (method git-fetch) (uri (git-reference @@ -17814,19 +18310,36 @@ module capable of computing base-level alignments for very large sequences.") (file-name (git-file-name name version)) (sha256 (base32 - "1j8mjnxcwn2xvzhf25lv4dbawxbgc4im1crh8081li7i4mbwswaj")))) + "1rf0p7dnakjry0fa6ax1h762bn0l5n6ibfdxn077mjvwgpqan51l")))) (build-system cmake-build-system) + (outputs '("out" "doc")) (arguments (list + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'set-HOME + ;; The build spams ‘Fontconfig error: No writable cache + ;; directories’ in a seemingly endless loop otherwise. + (lambda _ + (setenv "HOME" "/tmp")))) #:configure-flags #~(list "-DGDCM_BUILD_TESTING=true" (string-append "-DCMAKE_CTEST_ARGUMENTS=-E;" "'TestFileMetaInformation" "|TestElement2" "|TestSCUValidation" + "|TestWriter" + "|TestAnonymizer4" + "|TestPrinter1" "|TestEcho" - "|TestFind'")))) - (home-page "http://gdcm.sourceforge.net/wiki/index.php/Main_Page") + "|TestFind'") + "-DGDCM_DOCUMENTATION:BOOL=ON" + "-DGDCM_PDF_DOCUMENTATION:BOOL=OFF" + (string-append "-DGDCM_INSTALL_DOC_DIR=" + #$output:doc "/share/doc/" #$name) + "-DGDCM_BUILD_DOCBOOK_MANPAGES:BOOL=OFF"))) ; TODO: need ‘xsl-ns’ + (native-inputs (list doxygen graphviz)) + (home-page "https://gdcm.sourceforge.net/wiki/index.php/Main_Page") (synopsis "Grassroots DICOM library") (description "Grassroots DICOM (GDCM) is an implementation of the DICOM standard @@ -17835,7 +18348,7 @@ directly. GDCM includes a file format definition and a network communications protocol, both of which should be extended to provide a full set of tools for a researcher or small medical imaging vendor to interface with an existing medical database.") - (license license:bsd-2))) + (license license:bsd-3))) (define-public wiggletools (package |