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Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 152 |
1 files changed, 152 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6fea723fd8..426618147f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9,6 +9,7 @@ ;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com> ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net> +;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -12685,6 +12686,13 @@ once. This package provides tools to perform Drop-seq analyses.") `(#:parallel-tests? #f ; not supported #:phases (modify-phases %standard-phases + ;; "test.sh" runs STAR, which requires excessive amounts of memory. + (add-after 'unpack 'disable-resource-intensive-test + (lambda _ + (substitute* "Makefile.in" + (("(^ tests/test_trim_galore/test.sh).*" _ m) m) + (("^ test.sh") "")) + #t)) (add-after 'install 'wrap-executable ;; Make sure the executable finds all R modules. (lambda* (#:key inputs outputs #:allow-other-keys) @@ -12864,3 +12872,147 @@ data of bisulfite experiments; it produces reports on aggregate methylation and coverage and can be used to produce information on differential methylation and segmentation.") (license license:gpl3+))) + +(define-public pigx-scrnaseq + (package + (name "pigx-scrnaseq") + (version "0.0.2") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/" + "releases/download/v" version + "/pigx_scrnaseq-" version ".tar.gz")) + (sha256 + (base32 + "03gwp83823ji59y6nvyz89i4yd3faaqpc3791qia71i91470vfsg")))) + (build-system gnu-build-system) + (arguments + `(#:configure-flags + (list (string-append "PICARDJAR=" (assoc-ref %build-inputs "java-picard") + "/share/java/picard.jar") + (string-append "DROPSEQJAR=" (assoc-ref %build-inputs "dropseq-tools") + "/share/java/dropseq.jar")) + #:phases + (modify-phases %standard-phases + (add-after 'install 'wrap-executable + ;; Make sure the executable finds all R modules. + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (wrap-program (string-append out "/bin/pigx-scrnaseq") + `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))) + `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH"))))) + #t))))) + (inputs + `(("dropseq-tools" ,dropseq-tools) + ("fastqc" ,fastqc) + ("java-picard" ,java-picard) + ("java" ,icedtea-8) + ("python-wrapper" ,python-wrapper) + ("python-pyyaml" ,python-pyyaml) + ("python-pandas" ,python-pandas) + ("python-numpy" ,python-numpy) + ("python-loompy" ,python-loompy) + ("ghc-pandoc" ,ghc-pandoc) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) + ("snakemake" ,snakemake) + ("star" ,star) + ("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-singlecellexperiment" ,r-singlecellexperiment) + ("r-stringr" ,r-stringr) + ("r-yaml" ,r-yaml))) + (home-page "http://bioinformatics.mdc-berlin.de/pigx/") + (synopsis "Analysis pipeline for single-cell RNA sequencing experiments") + (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 +and interactive quality reports. The pipeline is designed to work with UMI +based methods.") + (license license:gpl3+))) + +(define-public pigx + (package + (name "pigx") + (version "0.0.1") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/BIMSBbioinfo/pigx/" + "releases/download/v" version + "/pigx-" version ".tar.gz")) + (sha256 + (base32 + "1nxb2hbp40yg3j7n56k4dhsd2fl1j8g0wpiiln56prqzljwnlgmf")))) + (build-system gnu-build-system) + (inputs + `(("python" ,python) + ("pigx-bsseq" ,pigx-bsseq) + ("pigx-chipseq" ,pigx-chipseq) + ("pigx-rnaseq" ,pigx-rnaseq) + ("pigx-scrnaseq" ,pigx-scrnaseq))) + (home-page "http://bioinformatics.mdc-berlin.de/pigx/") + (synopsis "Analysis pipelines for genomics") + (description "PiGx is a collection of genomics pipelines. It includes the +following pipelines: + +@itemize +@item PiGx BSseq for raw fastq read data of bisulfite experiments +@item PiGx RNAseq for RNAseq samples +@item PiGx scRNAseq for single cell dropseq analysis +@item PiGx ChIPseq for reads from ChIPseq experiments +@end itemize + +All pipelines are easily configured with a simple sample sheet and a +descriptive settings file. The result is a set of comprehensive, interactive +HTML reports with interesting findings about your samples.") + (license license:gpl3+))) + +(define-public r-diversitree + (package + (name "r-diversitree") + (version "0.9-10") + (source + (origin + (method url-fetch) + (uri (cran-uri "diversitree" version)) + (sha256 + (base32 + "0gh4rcrp0an3jh8915i1fsxlgyfk7njywgbd5ln5r2jhr085kpz7")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (inputs `(("fftw" ,fftw) ("gsl" ,gsl))) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-desolve" ,r-desolve) + ("r-rcpp" ,r-rcpp) + ("r-suplex" ,r-subplex))) + (home-page "https://www.zoology.ubc.ca/prog/diversitree") + (synopsis "Comparative 'phylogenetic' analyses of diversification") + (description "This package contains a number of comparative \"phylogenetic\" +methods, mostly focusing on analysing diversification and character evolution. +Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction) +and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and +Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods +include Markov models of discrete and continuous trait evolution and constant +rate speciation and extinction.") + (license license:gpl2+))) |