diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 647 |
1 files changed, 515 insertions, 132 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ada5965e5f..40ccba247c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8,7 +8,7 @@ ;;; 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> +;;; 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 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> @@ -4788,7 +4788,7 @@ performance.") "--enable-libcurl" "--enable-s3"))) (inputs - (list curl openssl)) + (list bzip2 curl openssl xz)) ;; This is referred to in the pkg-config file as a required library. (propagated-inputs (list zlib)) @@ -6668,7 +6668,7 @@ subsequent visualization, annotation and storage of results.") (define-public plink-ng (package (inherit plink) (name "plink-ng") - (version "2.00a2.3") + (version "2.00a3-20220315") (source (origin (method git-fetch) @@ -6677,7 +6677,7 @@ subsequent visualization, annotation and storage of results.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1p88lz9agzjlspjhciz61qjc36cfniv4nkxszyy0njqyc5rzc0cd")))) + (base32 "19inr47jwddkjb9kfb14yxc7xb16c73lkhgxj9sncb0fsiskb4x8")))) (build-system gnu-build-system) (arguments `(#:make-flags @@ -8981,6 +8981,34 @@ analysis, variant tools is project based and provides a whole set of tools to manipulate and analyze genetic variants.") (license license:gpl3+))) +(define-public r-chromvarmotifs + (let ((commit "38bed559c1f4770b6c91c80bf3f8ea965da26076") + (revision "1")) + (package + (name "r-chromvarmotifs") + (version (git-version "0.2.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/GreenleafLab/chromVARmotifs") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0i9v1m1hrg1lkd2pnkj5nnrpks6vhhhpbdhsfl2lmjak4npxxr5q")))) + (properties `((upstream-name . "chromVARmotifs"))) + (build-system r-build-system) + (propagated-inputs + `(("r-tfbstools" ,r-tfbstools))) + (home-page "https://github.com/GreenleafLab/chromVARmotifs") + (synopsis "Stores motif collections for use with motifmatchr or chromVAR") + (description + "This package stores motif collections as lists of @dfn{position +frequency matrix} (PWMatrixList) objects provided by the @code{TFBSTools} +package for use in R with packages like @code{motifmatchr} or +@code{chromVAR}.") + (license license:expat)))) + (define-public r-raremetals2 (package (name "r-raremetals2") @@ -9009,6 +9037,43 @@ for analyzing gene-level association tests in meta-analyses for binary trait.") (license license:gpl3))) +(define-public r-rnaseqdtu + (let ((commit "5bee1e769d2e1dc6a3f1cecb78078050eeb5b9ac") + (revision "1")) + (package + (name "r-rnaseqdtu") + (version (git-version "2.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mikelove/rnaseqDTU/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0jfi1ydsk8m5nadwnih48v87nnxdc7s3f0pny4axmnj40dd42as0")))) + (properties `((upstream-name . "rnaseqDTU"))) + (build-system r-build-system) + (propagated-inputs + (list r-deseq2 + r-devtools + r-dexseq + r-drimseq + r-edger + r-rafalib + r-stager)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/mikelove/rnaseqDTU/") + (synopsis "RNA-seq workflow for differential transcript usage") + (description + "This package provides an RNA-seq workflow for differential transcript +usage (DTU) following Salmon quantification. This workflow performs a DTU +analysis on simulated data. It also shows how to use stageR to perform +two-stage testing of DTU, a statistical framework to screen at the gene level +and then confirm which transcripts within the significant genes show evidence +of DTU.") + (license license:artistic2.0)))) + (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) @@ -9101,6 +9166,44 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") communication networks from scRNA-seq data.") (license license:gpl3)))) +(define-public r-copykat + (let ((commit ;no tag + "256de33dfc1b80a1a0ac9e098c5557f95a4e0d53") + (revision "0")) + (package + (name "r-copykat") + (version (git-version "1.0.8" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/navinlabcode/copykat") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ckyqnial3imcqlgd6xfgwk5w977l1i87sx4kdbwdvg40w0vh1j8")))) + (properties `((upstream-name . "copykat"))) + (build-system r-build-system) + (propagated-inputs + (list r-cluster + r-dlm + r-gplots + r-mcmcpack + r-mixtools + r-paralleldist + r-rcolorbrewer)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/navinlabcode/copykat") + (synopsis "Inference of genomic copy number from single cell RNAseq data") + (description + "This package Copynumber KAryotyping of Tumors infers genomic copy +number and subclonal structure of human tumors using integrative Bayesian +approaches to identify genome-wide aneuploidy at 5MB resolution in single +cells data. It separates tumor cells and tumor subclones from normal cells +using high-throughput sc-RNAseq data.") + (license license:gpl2)))) + (define-public sambamba (package (name "sambamba") @@ -10266,7 +10369,7 @@ variational inference.") (define-public python-loompy (package (name "python-loompy") - (version "2.0.17") + (version "3.0.7") ;; The tarball on Pypi does not include the tests. (source (origin (method git-fetch) @@ -10276,16 +10379,33 @@ variational inference.") (file-name (git-file-name name version)) (sha256 (base32 - "12a5kjgiikapv93wahfw0frszx1lblnppyz3vs5gy8fgmgngra07")))) + "0xmw2yv1y3y7vh5jcbrmlkn43nmfs0pf6z78k1yxqs3qy248m9b0")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases - (replace 'check + ;; See https://github.com/linnarsson-lab/loompy/issues/169 + (add-after 'unpack 'fix-h5py-error (lambda _ - (invoke "pytest" "tests")))))) + (substitute* "tests/test_file_attribute_manager.py" + (("h5py.File\\(f.name\\)") + "h5py.File(f.name, 'a')")))) + ;; 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 tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "tests"))))))) (propagated-inputs - (list python-h5py python-numpy python-pandas python-scipy)) + (list python-click + python-h5py + python-numba + python-numpy + python-numpy-groupies + python-pandas + python-scipy)) (native-inputs (list python-pytest)) (home-page "https://github.com/linnarsson-lab/loompy") @@ -10869,7 +10989,7 @@ once. This package provides tools to perform Drop-seq analyses.") (define-public pigx-rnaseq (package (name "pigx-rnaseq") - (version "0.0.19") + (version "0.0.20") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/" @@ -10877,8 +10997,7 @@ once. This package provides tools to perform Drop-seq analyses.") "/pigx_rnaseq-" version ".tar.gz")) (sha256 (base32 - "1ja3bda1appxrzbfy7wp7khy30mm7lic8xbq3gkbpc5bld3as9cm")) - (patches (search-patches "pigx-rnaseq-no-citeproc.patch")))) + "0bf65qqvlkc77vl7cmmzacq70f0qav4p6nf8pp3x1vdd0nvhr24f")))) (build-system gnu-build-system) (arguments `(#:parallel-tests? #f ; not supported @@ -10909,6 +11028,7 @@ once. This package provides tools to perform Drop-seq analyses.") sed gzip snakemake + megadepth multiqc star-for-pigx hisat2 @@ -11115,7 +11235,7 @@ methylation and segmentation.") (define-public pigx-scrnaseq (package (name "pigx-scrnaseq") - (version "1.1.7") + (version "1.1.8") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/" @@ -11123,65 +11243,63 @@ methylation and segmentation.") "/pigx_scrnaseq-" version ".tar.gz")) (sha256 (base32 - "1h5mcxzwj3cidlkvy9ly5wmi48vwfsjf8dxjfirknqxr9a92hwlx")) - (patches (search-patches "pigx-scrnaseq-no-citeproc.patch")))) + "1lc42hl8mz95kilh0z39s3wnv092mhm6vl2i394n0yfvdzk4f885")))) (build-system gnu-build-system) (arguments - `(#:phases + '(#:phases (modify-phases %standard-phases - (add-before 'bootstrap 'autoreconf - (lambda _ - (invoke "autoreconf" "-vif"))) - (add-before 'configure 'set-PYTHONPATH + (add-before 'configure 'set-additional-environment-variables (lambda _ + ;; Needed because of loompy + (setenv "NUMBA_CACHE_DIR" "/tmp") + ;; Needed to capture environment (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))))) - (native-inputs - (list automake autoconf)) (inputs - `(("coreutils" ,coreutils) - ("perl" ,perl) - ("fastqc" ,fastqc) - ("flexbar" ,flexbar) - ("java" ,icedtea-8) - ("jellyfish" ,jellyfish) - ("python-wrapper" ,python-wrapper) - ("python-pyyaml" ,python-pyyaml) - ("python-pandas" ,python-pandas) - ("python-magic" ,python-magic) - ("python-numpy" ,python-numpy) - ("python-loompy" ,python-loompy) - ("pandoc" ,pandoc) - ("samtools" ,samtools) - ("snakemake" ,snakemake) - ("star" ,star-for-pigx) - ("r-minimal" ,r-minimal) - ("r-argparser" ,r-argparser) - ("r-cowplot" ,r-cowplot) - ("r-data-table" ,r-data-table) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dplyr" ,r-dplyr) - ("r-dropbead" ,r-dropbead) - ("r-dt" ,r-dt) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-hdf5array" ,r-hdf5array) - ("r-pheatmap" ,r-pheatmap) - ("r-rmarkdown" ,r-rmarkdown) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-rtsne" ,r-rtsne) - ("r-scater" ,r-scater) - ("r-scran" ,r-scran) - ("r-seurat" ,r-seurat) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-stringr" ,r-stringr) - ("r-yaml" ,r-yaml))) + (list coreutils + perl + fastqc + flexbar + icedtea-8 + jellyfish + python-wrapper + python-pyyaml + python-pandas + python-magic + python-numpy + python-loompy + pandoc + samtools + snakemake + star-for-pigx + r-minimal + r-argparser + r-cowplot + r-data-table + r-delayedarray + r-delayedmatrixstats + r-dplyr + r-dropbead + r-dt + r-genomicalignments + r-genomicfiles + r-genomicranges + r-ggplot2 + r-hdf5array + r-pheatmap + r-rmarkdown + r-rsamtools + r-rtracklayer + r-rtsne + r-scater + r-scran + r-seurat + r-singlecellexperiment + r-stringr + r-yaml)) (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipeline for single-cell RNA sequencing experiments") - (description "PiGX scRNAseq is an analysis pipeline for preprocessing and + (description + "PiGX scRNAseq is an analysis pipeline for preprocessing and quality control for single cell RNA sequencing experiments. The inputs are read files from the sequencing experiment, and a configuration file which describes the experiment. It produces processed files for downstream analysis @@ -11192,7 +11310,7 @@ based methods.") (define-public pigx-sars-cov2-ww (package (name "pigx-sars-cov2-ww") - (version "0.0.4") + (version "0.0.5") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_sarscov2_ww/" @@ -11200,11 +11318,11 @@ based methods.") "/pigx_sars-cov2-ww-" version ".tar.gz")) (sha256 (base32 - "0axnmz4d8zgir888mc0cilcq4m3v41xmjmpp3w3444lciwnxydvs")) - (patches (search-patches "pigx-sars-cov2-ww-no-citeproc.patch")))) + "1fkr9gp09zl5n7kdqmy9lrnq28k2z97wg74wgkyfssfyxvmq9cr2")))) (build-system gnu-build-system) (arguments - `(#:phases + `(#:tests? #f ;requires huge kraken database + #:phases (modify-phases %standard-phases (add-before 'bootstrap 'autoreconf (lambda _ @@ -11813,6 +11931,105 @@ distributions. Homotypic doublet proportion estimation is achieved by finding the sum of squared cell annotation frequencies.") (license license:cc0)))) +;; There have been no releases. +(define-public r-cytobackbone + (let ((commit "4c1a0a35cc5ae1f8f516127cec92351d96fe26e7") + (revision "1")) + (package + (name "r-cytobackbone") + (version (git-version "1.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tchitchek-lab/CytoBackBone") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ahiad14zcgdk42xzw5xryic2ibn2l8lkrcdvl2b5sz2js028yb3")))) + (properties `((upstream-name . "CytoBackBone"))) + (build-system r-build-system) + (propagated-inputs + (list r-flowcore + r-flowutils + r-fnn + r-ggplot2 + r-preprocesscore)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/tchitchek-lab/CytoBackBone") + (synopsis "Merge phenotype information from different cytometric profiles") + (description + "This package implements an algorithm which increases the number of +simultaneously measurable markers and in this way helps with study of the +immune responses. Thus, the present algorithm, named @code{CytoBackBone}, +allows combining phenotypic information of cells from different cytometric +profiles obtained from different cytometry panels. This computational +approach is based on the principle that each cell has its own phenotypic and +functional characteristics that can be used as an identification card. +@code{CytoBackBone} uses a set of predefined markers, that we call the +backbone, to define this identification card. The phenotypic information of +cells with similar identification cards in the different cytometric profiles +is then merged.") + (license license:gpl2)))) + +(define-public r-giotto + (let ((commit "68d7390dce87223cac11d4d8f31705fe0144d011") + (revision "1")) + (package + (name "r-giotto") + (version (git-version "1.1.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/RubD/Giotto/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0mv60khc05wrxzr4ir6cirn7dpqvgwan5hm00lmafsyalr51nf5i")))) + (properties `((upstream-name . "Giotto"))) + (build-system r-build-system) + (propagated-inputs + (list r-clusterr + r-complexheatmap + r-cowplot + r-data-table + r-dbscan + r-deldir + r-farver + r-fitdistrplus + r-ggdendro + r-ggplot2 + r-ggraph + r-ggrepel + r-igraph + r-irlba + r-lfa + r-limma + r-magick + r-magrittr + r-matrix + r-matrixstats + r-plotly + r-qvalue + r-r-utils + r-rcolorbrewer + r-rcpp + r-reshape2 + r-reticulate + r-rfast + r-rlang + r-rtsne + r-scales + r-uwot)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/RubD/Giotto/") + (synopsis "Spatial single-cell transcriptomics toolbox") + (description + "This package provides a toolbox to process, analyze and visualize +spatial single-cell expression data.") + (license license:expat)))) + (define-public gffread ;; We cannot use the tagged release because it is not in sync with gclib. ;; See https://github.com/gpertea/gffread/issues/26 @@ -13461,6 +13678,13 @@ repeated areas between contigs.") (snippet '(for-each delete-file (find-files "." "\\.c"))))) (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")))))) (native-inputs (list python-joblib)) (propagated-inputs @@ -14116,51 +14340,59 @@ some of the details of opening and jumping in tabix-indexed files.") (base32 "0i9d8zrxpiracw3mxzd9siybpy62p06rqz9mc2w93arajgbk45bs")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; There are no tests to run. - #:make-flags '("libsw.a" "all") + (list + #:tests? #f ; There are no tests to run. + #:make-flags + #~(list (string-append "CXX=" #$(cxx-for-target)) + "libsw.a" "all") #:phases - (modify-phases %standard-phases - (delete 'configure) ; There is no configure phase. - (add-after 'unpack 'patch-source - (lambda _ - (substitute* "Makefile" - (("-c ") "-c -fPIC ")) - #t)) - (add-after 'build 'build-dynamic - (lambda _ - (invoke "g++" - "-shared" "-o" "libsmithwaterman.so" - "smithwaterman.o" "SmithWatermanGotoh.o" - "disorder.o" "BandedSmithWaterman.o" - "LeftAlign.o" "Repeats.o" "IndelAllele.o"))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin")) - (lib (string-append out "/lib"))) - (install-file "smithwaterman" bin) - (for-each - (lambda (file) - (install-file file (string-append out "/include/smithwaterman"))) - (find-files "." "\\.h$")) - (install-file "libsmithwaterman.so" lib) - (install-file "libsw.a" lib) - (mkdir-p (string-append lib "/pkgconfig")) - (with-output-to-file (string-append lib "/pkgconfig/smithwaterman.pc") - (lambda _ - (format #t "prefix=~a~@ - exec_prefix=${prefix}~@ - libdir=${exec_prefix}/lib~@ - includedir=${prefix}/include/smithwaterman~@ - ~@ - ~@ - Name: smithwaterman~@ - Version: ~a~@ - Description: smith-waterman-gotoh alignment algorithm~@ - Libs: -L${libdir} -lsmithwaterman~@ - Cflags: -I${includedir}~%" - out ,version)))) - #t))))) + #~(modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (add-after 'unpack 'patch-source + (lambda _ + (substitute* "Makefile" + (("-c ") "-c -fPIC ")) + #$@(if (%current-target-system) + #~((substitute* "Makefile" + (("\tld") + (string-append "\t" #$(%current-target-system) "-ld")) + (("\tar") + (string-append "\t" #$(%current-target-system) "-ar")))) + '()))) + (add-after 'build 'build-dynamic + (lambda _ + (invoke #$(cxx-for-target) + "-shared" "-o" "libsmithwaterman.so" + "smithwaterman.o" "SmithWatermanGotoh.o" + "disorder.o" "BandedSmithWaterman.o" + "LeftAlign.o" "Repeats.o" "IndelAllele.o"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (lib (string-append out "/lib"))) + (install-file "smithwaterman" bin) + (for-each + (lambda (file) + (install-file file (string-append out "/include/smithwaterman"))) + (find-files "." "\\.h$")) + (install-file "libsmithwaterman.so" lib) + (install-file "libsw.a" lib) + (mkdir-p (string-append lib "/pkgconfig")) + (with-output-to-file (string-append lib "/pkgconfig/smithwaterman.pc") + (lambda _ + (format #t "prefix=~a~@ + exec_prefix=${prefix}~@ + libdir=${exec_prefix}/lib~@ + includedir=${prefix}/include/smithwaterman~@ + ~@ + ~@ + Name: smithwaterman~@ + Version: ~a~@ + Description: smith-waterman-gotoh alignment algorithm~@ + Libs: -L${libdir} -lsmithwaterman~@ + Cflags: -I${includedir}~%" + out #$version))))))))) (home-page "https://github.com/ekg/smithwaterman") (synopsis "Implementation of the Smith-Waterman algorithm") (description "Implementation of the Smith-Waterman algorithm.") @@ -14304,7 +14536,7 @@ library automatically handles index file generation and use.") (define-public vcflib (package (name "vcflib") - (version "1.0.2") + (version "1.0.3") (source (origin (method git-fetch) @@ -14313,7 +14545,7 @@ library automatically handles index file generation and use.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1k1z3876kbzifj1sqfzsf3lgb4rw779hvkg6ryxbyq5bc2paj9kh")) + (base32 "1r7pnajg997zdjkf1b38m14v0zqnfx52w7nbldwh1xpbpahb1hjh")) (modules '((guix build utils))) (snippet '(begin @@ -14336,8 +14568,7 @@ library automatically handles index file generation and use.") (("Fasta.h") "fastahack/Fasta.h")) (for-each delete-file-recursively '("fastahack" "filevercmp" "fsom" "googletest" "intervaltree" - "libVCFH" "multichoose" "smithwaterman")) - #t)))) + "libVCFH" "multichoose" "smithwaterman")))))) (build-system cmake-build-system) (inputs (list bzip2 @@ -14366,8 +14597,7 @@ library automatically handles index file generation and use.") (substitute* "CMakeLists.txt" (("vcflib STATIC") "vcflib SHARED")) (substitute* "test/Makefile" - (("libvcflib.a") "libvcflib.so")) - #t)) + (("libvcflib.a") "libvcflib.so")))) (add-after 'unpack 'unpack-submodule-sources (lambda* (#:key inputs #:allow-other-keys) (let ((unpack (lambda (source target) @@ -14382,8 +14612,7 @@ library automatically handles index file generation and use.") (unpack "filevercmp-src" "filevercmp") (unpack "fsom-src" "fsom") (unpack "intervaltree-src" "intervaltree") - (unpack "multichoose-src" "multichoose")) - #t))) + (unpack "multichoose-src" "multichoose"))))) ;; This pkg-config file is provided by other distributions. (add-after 'install 'install-pkg-config-file (lambda* (#:key outputs #:allow-other-keys) @@ -14441,6 +14670,7 @@ manipulations on VCF files.") ("parallel" ,parallel) ("perl" ,perl) ("pkg-config" ,pkg-config) + ("python" ,python) ("samtools" ,samtools) ("simde" ,simde) ;; This submodule is needed to run the tests. @@ -15275,11 +15505,11 @@ translates between different variant encodings.") (license license:asl2.0)))) (define-public r-signac - (let ((commit "e0512d348adeda4a3f23a2e8f56d1fe09840e03c") - (revision "1")) + (let ((commit "458e647b503c3472b0b98c0aeca934f452e039ee") + (revision "2")) (package (name "r-signac") - (version (git-version "1.1.1" revision commit)) + (version (git-version "1.6.0" revision commit)) (source (origin (method git-fetch) @@ -15288,16 +15518,12 @@ translates between different variant encodings.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 - "1yihhrv7zs87ax61la1nb4y12lg3knraw4b20k5digbcwm8488lb")))) + (base32 "1hgwpgighkvfkai80n4d2252s4sdpa4faag4ncdiylicl5wa7lbj")))) (properties `((upstream-name . "Signac"))) (build-system r-build-system) (inputs (list zlib)) (propagated-inputs - (list r-annotationfilter - r-biocgenerics - r-biostrings - r-biovizbase + (list r-biocgenerics r-data-table r-dplyr r-fastmatch @@ -15305,7 +15531,6 @@ translates between different variant encodings.") r-future-apply r-genomeinfodb r-genomicranges - r-ggbio r-ggforce r-ggplot2 r-ggrepel @@ -15316,6 +15541,7 @@ translates between different variant encodings.") r-matrix r-patchwork r-pbapply + r-qlcmatrix r-rcpp r-rcpproll r-rsamtools @@ -15324,7 +15550,8 @@ translates between different variant encodings.") r-seurat r-seuratobject r-stringi - r-tidyr)) + r-tidyr + r-tidyselect)) (home-page "https://github.com/timoast/signac/") (synopsis "Analysis of single-cell chromatin data") (description @@ -15722,7 +15949,11 @@ populations.") (file-name (git-file-name name version)) (sha256 (base32 - "1k8hllr5if6k2mm2zj391fv40sfc008cjm04l9vgfsdppb80i112")))) + "1k8hllr5if6k2mm2zj391fv40sfc008cjm04l9vgfsdppb80i112")) + (snippet + #~(begin + (use-modules ((guix build utils))) + (delete-file "src/scregseg/_utils.c"))))) (build-system python-build-system) (arguments `(#:tests? #false ; tests require network access @@ -16069,3 +16300,155 @@ workflows from concise descriptions in ccwl. It is implemented as an @acronym{EDSL, Embedded Domain Specific Language} in the Scheme programming language.") (license license:gpl3+))) + +(define-public wfmash + (package + (name "wfmash") + (version "0.8.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/ekg/wfmash/releases/download/v" + version "/wfmash-v" version ".tar.gz")) + (sha256 + (base32 + "031cm1arpfckvihb28vlk69mirpnmlag81zcscfba1bac58wvr7c")) + (snippet + #~(begin + (use-modules (guix build utils)) + ;; Unbundle atomic-queue. + (delete-file-recursively "src/common/atomic_queue") + (substitute* "src/align/include/computeAlignments.hpp" + (("\"common/atomic_queue/atomic_queue.h\"") + "<atomic_queue/atomic_queue.h>")) + ;; Remove compiler optimizations. + (substitute* (find-files "." "CMakeLists\\.txt") + (("-mcx16 ") "") + (("-march=native ") "")) + ;; Allow building on architectures other than x86_64. + (substitute* "src/common/dset64.hpp" + (("!__x86_64__") "0")))))) + (build-system cmake-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + ;; Adapted from .github/workflows/test_on_push.yml + (lambda* (#:key tests? inputs #:allow-other-keys) + (when tests? + (let ((samtools (search-input-file inputs "/bin/samtools"))) + ;; This is the easiest way to access the data + ;; needed for the test suite. + (symlink (string-append "../wfmash-v" #$version "/data") + "data") + (and + ;; This test takes 60 minutes on riscv64-linux. + #$@(if (not (target-riscv64?)) + #~((begin + ;; Test with a subset of the LPA dataset (PAF output) + (setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1") + (setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1") + (with-output-to-file "LPA.subset.paf" + (lambda _ + (invoke "bin/wfmash" + "data/LPA.subset.fa.gz" + "data/LPA.subset.fa.gz" + "-X" "-n" "10" "-T" "wflign_info." + "-u" "./"))) + (invoke "head" "LPA.subset.paf"))) + #~()) + ;; This test takes about 5 hours on riscv64-linux. + #$@(if (not (target-riscv64?)) + #~((begin + ;; Test with a subset of the LPA dataset (SAM output) + (setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1") + (setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1") + (with-output-to-file "LPA.subset.sam" + (lambda _ + (invoke "bin/wfmash" + "data/LPA.subset.fa.gz" + "data/LPA.subset.fa.gz" + "-X" "-N" "-a" "-T" "wflign_info."))) + (with-output-to-file "LPA.subset.sam-view" + (lambda _ + (invoke samtools "view" "LPA.subset.sam" "-bS"))) + (with-output-to-file "LPA.subset.bam" + (lambda _ + (invoke samtools "sort" "LPA.subset.sam-view"))) + (invoke samtools "index" "LPA.subset.bam") + ;; samtools view LPA.subset.bam | head | cut -f 1-9 + ;(invoke samtools "view" "LPA.subset.bam") + ;; There should be an easier way to do this with pipes. + (with-output-to-file "LPA.subset.bam-incr1" + (lambda _ + (invoke samtools "view" "LPA.subset.bam"))) + (with-output-to-file "LPA.subset.bam-incr2" + (lambda _ + (invoke "head" "LPA.subset.bam-incr1"))) + (invoke "cut" "-f" "1-9" "LPA.subset.bam-incr2"))) + #~()) + ;; This test takes 60 minutes on riscv64-linux. + #$@(if (not (target-riscv64?)) + #~((begin + ;; Test with a subset of the LPA dataset, + ;; setting a lower identity threshold (PAF output) + (setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1") + (setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1") + (with-output-to-file "LPA.subset.p90.paf" + (lambda _ + (invoke "bin/wfmash" + "data/LPA.subset.fa.gz" + "data/LPA.subset.fa.gz" + "-X" "-p" "90" "-n" "10" + "-T" "wflign_info."))) + (invoke "head" "LPA.subset.p90.paf"))) + #~()) + (begin + ;; Test aligning short reads (500 bps) to a reference (SAM output) + (setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1") + (setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1") + (with-output-to-file "reads.500bps.sam" + (lambda _ + (invoke "bin/wfmash" + "data/reference.fa.gz" + "data/reads.500bps.fa.gz" + "-s" "0.5k" "-N" "-a"))) + (with-output-to-file "reads.500bps.sam-view" + (lambda _ + (invoke samtools "view" "reads.500bps.sam" "-bS"))) + (with-output-to-file "reads.500bps.bam" + (lambda _ + (invoke samtools "sort" "reads.500bps.sam-view"))) + (invoke samtools "index" "reads.500bps.bam") + (with-output-to-file "reads.500bps.bam-view" + (lambda _ + (invoke samtools "view" "reads.500bps.bam"))) + (invoke "head" "reads.500bps.bam-view")) + (begin + ;; Test with few very short reads (255bps) (PAF output) + (setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1") + (setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1") + (with-output-to-file "reads.255bps.paf" + (lambda _ + (invoke "bin/wfmash" + "data/reads.255bps.fa.gz" + "data/reads.255bps.fa.gz" + "-X" "-w" "16"))) + (invoke "head" "reads.255bps.paf")))))))))) + (inputs + (list atomic-queue + gsl + htslib + jemalloc + zlib)) + (native-inputs + (list samtools)) + (synopsis "Base-accurate DNA sequence aligner") + (description "@code{wfmash} is a DNA sequence read mapper based on mash +distances and the wavefront alignment algorithm. It is a fork of MashMap that +implements base-level alignment via the wflign tiled wavefront global +alignment algorithm. It completes MashMap with a high-performance alignment +module capable of computing base-level alignments for very large sequences.") + (home-page "https://github.com/ekg/wfmash") + (license license:expat))) |