diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 348 |
1 files changed, 321 insertions, 27 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 73765dafe7..78754793a5 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. ;;; @@ -110,32 +111,6 @@ #:use-module (srfi srfi-1) #:use-module (ice-9 match)) -(define-public r-ape - (package - (name "r-ape") - (version "5.0") - (source - (origin - (method url-fetch) - (uri (cran-uri "ape" version)) - (sha256 - (base32 - "0q59pmxawz498cb9mv5m49lhiwxib8ak94yyydz7qg8b6lpd4bn3")))) - (build-system r-build-system) - (propagated-inputs - `(("r-lattice" ,r-lattice) - ("r-nlme" ,r-nlme) - ("r-rcpp" ,r-rcpp))) - (home-page "http://ape-package.ird.fr/") - (synopsis "Analyses of phylogenetics and evolution") - (description - "This package provides functions for reading, writing, plotting, and -manipulating phylogenetic trees, analyses of comparative data in a -phylogenetic framework, ancestral character analyses, analyses of -diversification and macroevolution, computing distances from DNA sequences, -and several other tools.") - (license license:gpl2+))) - (define-public aragorn (package (name "aragorn") @@ -10680,6 +10655,16 @@ block processing.") (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) (rename-file (string-append "hdf5-" ,(package-version hdf5)) "hdf5") + ;; Remove timestamp and host system information to make + ;; the build reproducible. + (substitute* "hdf5/src/libhdf5.settings.in" + (("Configured on: @CONFIG_DATE@") + "Configured on: Guix") + (("Uname information:.*") + "Uname information: Linux\n") + ;; Remove unnecessary store reference. + (("C Compiler:.*") + "C Compiler: GCC\n")) (rename-file "Makevars.in" "Makevars") (substitute* "Makevars" (("HDF5_CXX_LIB=.*") @@ -10879,6 +10864,34 @@ are optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.") (license license:expat))) +(define-public r-phangorn + (package + (name "r-phangorn") + (version "2.4.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "phangorn" version)) + (sha256 + (base32 + "0xc8k552nxczy19jr0xjjagrzc8x6lafasgk2c099ls8bc1yml1i")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-fastmatch" ,r-fastmatch) + ("r-igraph" ,r-igraph) + ("r-magrittr" ,r-magrittr) + ("r-matrix" ,r-matrix) + ("r-quadprog" ,r-quadprog) + ("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/KlausVigo/phangorn") + (synopsis "Phylogenetic analysis in R") + (description + "Phangorn is a package for phylogenetic analysis in R. It supports +estimation of phylogenetic trees and networks using Maximum Likelihood, +Maximum Parsimony, distance methods and Hadamard conjugation.") + (license license:gpl2+))) + (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) @@ -11407,7 +11420,7 @@ models. TADbit is complemented by TADkit for visualizing 3D models.") ("tcsh" ,tcsh) ("perl" ,perl) ("libpng" ,libpng) - ("mysql" ,mysql) + ("mariadb" ,mariadb) ("openssl" ,openssl))) (home-page "http://genome.cse.ucsc.edu/index.html") (synopsis "Assorted bioinformatics utilities") @@ -12664,6 +12677,13 @@ 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) @@ -12713,3 +12733,277 @@ and a configuration file which describes the experiment. In addition to quality control of the experiment, the pipeline produces a differential expression report comparing samples in an easily configurable manner.") (license license:gpl3+))) + +(define-public pigx-chipseq + (package + (name "pigx-chipseq") + (version "0.0.2") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/" + "releases/download/v" version + "/pigx_chipseq-" version ".tar.gz")) + (sha256 + (base32 + "1jliwhifnjgl9x0z730bzpxswi2s84fyg5y8cagbyzpw509452f5")))) + (build-system gnu-build-system) + (arguments + `(#: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-chipseq") + `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))) + `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH"))))) + #t))))) + (inputs + `(("r-minimal" ,r-minimal) + ("r-argparser" ,r-argparser) + ("r-chipseq" ,r-chipseq) + ("r-data-table" ,r-data-table) + ("r-genomation" ,r-genomation) + ("r-genomicranges" ,r-genomicranges) + ("r-rtracklayer" ,r-rtracklayer) + ("r-rcas" ,r-rcas) + ("r-stringr" ,r-stringr) + ("r-jsonlite" ,r-jsonlite) + ("r-heatmaply" ,r-heatmaply) + ("r-ggplot2" ,r-ggplot2) + ("r-plotly" ,r-plotly) + ("python-wrapper" ,python-wrapper) + ("python-pyyaml" ,python-pyyaml) + ("snakemake" ,snakemake) + ("macs" ,macs) + ("multiqc" ,multiqc) + ("perl" ,perl) + ("ghc-pandoc" ,ghc-pandoc) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) + ("fastqc" ,fastqc) + ("bowtie" ,bowtie) + ("idr" ,idr) + ("snakemake" ,snakemake) + ("samtools" ,samtools) + ("bedtools" ,bedtools) + ("kentutils" ,kentutils))) + (native-inputs + `(("python-pytest" ,python-pytest))) + (home-page "http://bioinformatics.mdc-berlin.de/pigx/") + (synopsis "Analysis pipeline for ChIP sequencing experiments") + (description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak +calling and reporting for ChIP sequencing experiments. It is easy to use and +produces high quality reports. The inputs are reads files from the sequencing +experiment, and a configuration file which describes the experiment. In +addition to quality control of the experiment, the pipeline enables to set up +multiple peak calling analysis and allows the generation of a UCSC track hub +in an easily configurable manner.") + (license license:gpl3+))) + +(define-public pigx-bsseq + (package + (name "pigx-bsseq") + (version "0.0.5") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/" + "releases/download/v" version + "/pigx_bsseq-" version ".tar.gz")) + (sha256 + (base32 + "1h8ma99vi7hs83nafvjpq8jmaq9977j3n11c4zd95hai0cf7zxmp")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'check 'set-timezone + ;; The readr package is picky about timezones. + (lambda* (#:key inputs #:allow-other-keys) + (setenv "TZ" "UTC+1") + (setenv "TZDIR" + (string-append (assoc-ref inputs "tzdata") + "/share/zoneinfo")) + #t)) + (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-bsseq") + `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))) + `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH"))))) + #t))))) + (native-inputs + `(("tzdata" ,tzdata))) + (inputs + `(("r-minimal" ,r-minimal) + ("r-annotationhub" ,r-annotationhub) + ("r-dt" ,r-dt) + ("r-genomation" ,r-genomation) + ("r-methylkit" ,r-methylkit) + ("r-rtracklayer" ,r-rtracklayer) + ("r-rmarkdown" ,r-rmarkdown) + ("r-bookdown" ,r-bookdown) + ("r-ggplot2" ,r-ggplot2) + ("r-ggbio" ,r-ggbio) + ("ghc-pandoc" ,ghc-pandoc) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) + ("python-wrapper" ,python-wrapper) + ("python-pyyaml" ,python-pyyaml) + ("snakemake" ,snakemake) + ("bismark" ,bismark) + ("fastqc" ,fastqc) + ("bowtie" ,bowtie) + ("trim-galore" ,trim-galore) + ("cutadapt" ,cutadapt) + ("samtools" ,samtools))) + (home-page "http://bioinformatics.mdc-berlin.de/pigx/") + (synopsis "Bisulfite sequencing pipeline from fastq to methylation reports") + (description "PiGx BSseq is a data processing pipeline for raw fastq read +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+))) |