diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 115 |
1 files changed, 60 insertions, 55 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0e4cb5b1db..e8dac2a12b 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 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> @@ -261,7 +261,7 @@ structure of the predicted RNA.") ("coreutils" ,coreutils))) (propagated-inputs `(("python-numpy" ,python2-numpy))) - (home-page "http://ecogenomics.github.io/BamM/") + (home-page "https://ecogenomics.github.io/BamM/") (synopsis "Metagenomics-focused BAM file manipulator") (description "BamM is a C library, wrapped in python, to efficiently generate and @@ -726,7 +726,7 @@ provides the Ribotaper pipeline.") (native-inputs `(("python-mock" ,python2-mock) ("python-nose" ,python2-nose))) - (home-page "http://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/") + (home-page "https://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/") (synopsis "Detect translation efficiency changes from ribosome footprints") (description "RiboDiff is a statistical tool that detects the protein translational efficiency change from Ribo-Seq (ribosome footprinting) and @@ -1056,7 +1056,7 @@ provide a coordinated and extensible framework to do computational biology.") (lambda _ (setenv "HOME" "/tmp") #t))))) (propagated-inputs `(("python-numpy" ,python-numpy))) - (home-page "http://biopython.org/") + (home-page "https://biopython.org/") (synopsis "Tools for biological computation in Python") (description "Biopython is a set of tools for biological computation including parsers @@ -2439,7 +2439,7 @@ accessing bigWig files.") (base32 "097hfyv2kaf4x92i4rjx0paw2cncxap48qivv8zxng4z7nhid0x9")))) (build-system python-build-system) - (home-page "http://packages.python.org/DendroPy/") + (home-page "https://dendropy.org/") (synopsis "Library for phylogenetics and phylogenetic computing") (description "DendroPy is a library for phylogenetics and phylogenetic computing: reading, @@ -2676,7 +2676,7 @@ data and settings.") texlive-latex-pgf ; tikz texlive-latex-verbatimbox))) ("imagemagick" ,imagemagick))) - (home-page "http://dorina.mdc-berlin.de/public/rajewsky/discrover/") + (home-page "https://dorina.mdc-berlin.de/public/rajewsky/discrover/") (synopsis "Discover discriminative nucleotide sequence motifs") (description "Discrover is a motif discovery method to find binding sites of nucleic acid binding proteins.") @@ -2796,7 +2796,7 @@ quantitative phenotypes.") ("perl-www-robotrules" ,perl-www-robotrules) ("perl-xml-simple" ,perl-xml-simple) ("perl" ,perl))) - (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/") + (home-page "https://www.ncbi.nlm.nih.gov/books/NBK179288/") (synopsis "Tools for accessing the NCBI's set of databases") (description "Entrez Direct (EDirect) is a method for accessing the National Center @@ -2916,7 +2916,7 @@ ChIP-Seq, and analysis of metagenomic data.") #t)))))) (inputs `(("python" ,python-2))) - (home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity") + (home-page "https://github.com/dparks1134/ExpressBetaDiversity") (synopsis "Taxon- and phylogenetic-based beta diversity measures") (description "Express Beta Diversity (EBD) calculates ecological beta diversity @@ -3313,7 +3313,8 @@ association studies (GWAS).") ("python-networkx" ,python2-networkx))) (native-inputs `(("python-cython" ,python2-cython))) - (home-page "http://grit-bio.org") + ;; The canonical <http://grit-bio.org> home page times out as of 2020-01-21. + (home-page "https://github.com/nboley/grit") (synopsis "Tool for integrative analysis of RNA-seq type assays") (description "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify @@ -3380,7 +3381,7 @@ estimates transcript expression.") ;; Non-portable SSE instructions are used so building fails on platforms ;; other than x86_64. (supported-systems '("x86_64-linux")) - (home-page "http://ccb.jhu.edu/software/hisat/index.shtml") + (home-page "https://ccb.jhu.edu/software/hisat/index.shtml") (synopsis "Hierarchical indexing for spliced alignment of transcripts") (description "HISAT is a fast and sensitive spliced alignment program for mapping @@ -3434,7 +3435,7 @@ particular, reads spanning multiple exons.") `(("unzip" ,unzip) ; needed for archive from ftp ("perl" ,perl) ("pandoc" ,ghc-pandoc))) ; for documentation - (home-page "http://ccb.jhu.edu/software/hisat2/index.shtml") + (home-page "https://ccb.jhu.edu/software/hisat2/index.shtml") (synopsis "Graph-based alignment of genomic sequencing reads") (description "HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human @@ -3494,7 +3495,7 @@ HMMs).") (inputs `(("python-pysam" ,python-pysam) ("python-matplotlib" ,python-matplotlib))) - (home-page "http://www-huber.embl.de/users/anders/HTSeq/") + (home-page "https://htseq.readthedocs.io/") (synopsis "Analysing high-throughput sequencing data with Python") (description "HTSeq is a Python package that provides infrastructure to process data @@ -3969,7 +3970,7 @@ VCF.") ("java-jbzip2" ,java-jbzip2))) (native-inputs `(("unzip" ,unzip))) - (home-page "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/") + (home-page "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/") (synopsis "Quality control tool for high throughput sequence data") (description "FastQC aims to provide a simple way to do some quality control @@ -4048,7 +4049,7 @@ performance.") `(("zlib" ,zlib))) (native-inputs `(("perl" ,perl))) - (home-page "http://www.htslib.org") + (home-page "https://www.htslib.org") (synopsis "C library for reading/writing high-throughput sequencing data") (description "HTSlib is a C library for reading/writing high-throughput sequencing @@ -4595,7 +4596,7 @@ assembled metagenomic sequence.") ;; Use setuptools, or else the executables are not ;; installed. (("distutils.core") "setuptools") - ;; use "gcc" instead of "cc" for compilation + ;; Use "gcc" instead of "cc" for compilation. (("^defines") "cc.set_executables( compiler='gcc', @@ -4605,8 +4606,8 @@ linker_so='gcc -shared'); defines")) #t)))) (build-system python-build-system) (arguments - `(#:python ,python-2 ; only Python 2 is supported - #:tests? #f)) ; no "test" target + `(#:python ,python-2 ; only Python 2 is supported + #:tests? #f)) ; no "test" target (inputs `(("samtools" ,samtools) ("python-numpy" ,python2-numpy) @@ -4614,9 +4615,9 @@ linker_so='gcc -shared'); defines")) ("python-scipy" ,python2-scipy) ("python-matplotlib" ,python2-matplotlib))) (native-inputs - `(("python-mock" ,python2-mock) ;for tests - ("python-pytz" ,python2-pytz))) ;for tests - (home-page "http://genes.mit.edu/burgelab/miso/index.html") + `(("python-mock" ,python2-mock) ; for tests + ("python-pytz" ,python2-pytz))) ; for tests + (home-page "https://www.genes.mit.edu/burgelab/miso/index.html") (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation") (description "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates @@ -4742,7 +4743,7 @@ interrupted by stop codons. OrfM finds and prints these ORFs.") `(("python-nose" ,python2-nose) ("python-sphinx" ,python2-sphinx) ("python-pyxb" ,python2-pyxb))) - (home-page "http://pacificbiosciences.github.io/pbcore/") + (home-page "https://pacificbiosciences.github.io/pbcore/") (synopsis "Library for reading and writing PacBio data files") (description "The pbcore package provides Python APIs for interacting with PacBio data @@ -4991,6 +4992,8 @@ different command-line tools: (define-public prodigal (package (name "prodigal") + ;; Check for a new home page when updating this package: + ;; https://github.com/hyattpd/Prodigal/issues/36#issuecomment-536617588 (version "2.6.3") (source (origin (method git-fetch) @@ -5003,14 +5006,14 @@ different command-line tools: "1fs1hqk83qjbjhrvhw6ni75zakx5ki1ayy3v6wwkn3xvahc9hi5s")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ;no check target + `(#:tests? #f ; no check target #:make-flags (list (string-append "INSTALLDIR=" (assoc-ref %outputs "out") "/bin")) #:phases (modify-phases %standard-phases (delete 'configure)))) - (home-page "http://prodigal.ornl.gov") + (home-page "https://github.com/hyattpd/Prodigal") (synopsis "Protein-coding gene prediction for Archaea and Bacteria") (description "Prodigal runs smoothly on finished genomes, draft genomes, and @@ -5124,7 +5127,7 @@ partial genes, and identifies translation initiation sites.") ("r-minimal" ,r-minimal) ("r-ggplot2" ,r-ggplot2) ("coreutils" ,coreutils))) - (home-page "http://sanger-pathogens.github.io/Roary") + (home-page "https://sanger-pathogens.github.io/Roary/") (synopsis "High speed stand-alone pan genome pipeline") (description "Roary is a high speed stand alone pan genome pipeline, which takes @@ -5168,7 +5171,7 @@ extremely diverse sets of genomes.") #t))))) (inputs `(("openmpi" ,openmpi))) - (home-page "http://sco.h-its.org/exelixis/web/software/raxml/index.html") + (home-page "https://cme.h-its.org/exelixis/web/software/raxml/index.html") (synopsis "Randomized Axelerated Maximum Likelihood phylogenetic trees") (description "RAxML is a tool for phylogenetic analysis and post-analysis of large @@ -6039,7 +6042,8 @@ sequence itself can be retrieved from these databases.") ("fuse" ,fuse) ("hdf5" ,hdf5) ("zlib" ,zlib))) - (home-page "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software") + (home-page + "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software") (synopsis "Tools and libraries for reading and writing sequencing data") (description "The SRA Toolkit from NCBI is a collection of tools and libraries for @@ -6265,7 +6269,7 @@ of these reads to align data quickly through a hash-based indexing scheme.") #t)))))) (inputs `(("zlib" ,zlib))) - (home-page "http://bioinfo.lifl.fr/RNA/sortmerna") + (home-page "https://bioinfo.lifl.fr/RNA/sortmerna/") (synopsis "Biological sequence analysis tool for NGS reads") (description "SortMeRNA is a biological sequence analysis tool for filtering, mapping @@ -7272,13 +7276,13 @@ also known as views, in a controlled vocabulary.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.14.2") + (version "2.14.4") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "0nc1cbzp5zdwc0rss4r6v7cpgynmmnj3sczwmajr58nabkndwsvf")))) + "1x71in059zql40f4c87bd1gf96r945kdvwbq61jmch9d3d8nwxbb")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) @@ -7345,13 +7349,13 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.24.1") + (version "0.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "1rr7ml3gn83g8fbvhgvryyzlh4p3qgpwcrsz6ii4y7gh1hqxggpx")))) + "1s1h00k2ki7sd0hz4l8n41xr6ixszag7lm0ryrbb08idgcy16ipn")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -7372,13 +7376,13 @@ S4Vectors package itself.") (define-public r-iranges (package (name "r-iranges") - (version "2.20.1") + (version "2.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "0qssp04wfrc1r92hd3szy03n8sdz8vrqjdxa2mcrsc0k0n9bchz5")))) + "1jhnxb9yacmj2z82b6992gihjvj1a0gnjwbjiagyyx03fqnv23kg")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -7783,13 +7787,13 @@ tab-delimited (tabix) files.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.12.1") + (version "0.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "1yr4i2x127v814nxg53aibp77p3vg76f3n3hgknpwx3snfhc81xs")))) + "09lackgix5jpm16k0mz2zkibflfb4wzidbz4q32mlxmklf40037q")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -8233,7 +8237,7 @@ throughput genetic sequencing data sets using regression methods.") (base32 "03lmvydln8b7666b6w46qbryhf83vsd11d4y2v95rfgvqgq66l1i")))) (build-system r-build-system) - (home-page "http://rqtl.org/") + (home-page "https://rqtl.org/") (synopsis "R package for analyzing QTL experiments in genetics") (description "R/qtl is an extension library for the R statistics system. It is used to analyze experimental crosses for identifying @@ -8309,7 +8313,7 @@ libraries for systems that do not have these available via other means.") (propagated-inputs `(("r-optparse" ,r-optparse) ("r-rcolorbrewer" ,r-rcolorbrewer))) - (home-page "http://www.e-rna.org/r-chie/index.cgi") + (home-page "https://www.e-rna.org/r-chie/index.cgi") (synopsis "Analysis framework for RNA secondary structure") (description "The R4RNA package aims to be a general framework for the analysis of RNA @@ -8929,7 +8933,7 @@ replacement for strverscmp.") (("['\"]matplotlib.*?['\"]") "'matplotlib'")) #t))))) - (home-page "http://multiqc.info") + (home-page "https://multiqc.info") (synopsis "Aggregate bioinformatics analysis reports") (description "MultiQC is a tool to aggregate bioinformatics results across many @@ -9599,7 +9603,7 @@ classes.") ("r-locfit" ,r-locfit) ("r-mass" ,r-mass) ("r-rcolorbrewer" ,r-rcolorbrewer))) - (home-page "http://www-huber.embl.de/users/anders/DESeq") + (home-page "https://www-huber.embl.de/users/anders/DESeq/") (synopsis "Differential gene expression analysis") (description "This package provides tools for estimating variance-mean dependence in @@ -9728,7 +9732,7 @@ by the user, helping with quick and reproducible access.") ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-s4vectors" ,r-s4vectors))) - (home-page "http://www.bioinf.jku.at/software/fastseg/index.html") + (home-page "https://www.bioinf.jku.at/software/fastseg/index.html") (synopsis "Fast segmentation algorithm for genetic sequencing data") (description "Fastseg implements a very fast and efficient segmentation algorithm. @@ -9780,7 +9784,8 @@ microarrays or GRanges for sequencing data.") `(("r-annotationdbi" ,r-annotationdbi) ("r-graph" ,r-graph) ("r-keggrest" ,r-keggrest))) - (home-page "http://www.biomedcentral.com/1471-2105/10/161") + (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/" + "articles/10.1186/1471-2105-10-161")) (synopsis "Generally applicable gene-set enrichment for pathway analysis") (description "GAGE is a published method for gene set (enrichment or GSEA) or pathway @@ -10161,7 +10166,7 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.") (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "http://www.bioconductor.org/packages/" + (uri (string-append "https://www.bioconductor.org/packages/" "release/data/annotation/src/contrib/" "Homo.sapiens_" version ".tar.gz")) @@ -10892,7 +10897,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (inputs `(("lz4" ,lz4) ("htslib" ,htslib-for-sambamba))) - (home-page "http://lomereiter.github.io/sambamba") + (home-page "https://lomereiter.github.io/sambamba/") (synopsis "Tools for working with SAM/BAM data") (description "Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for @@ -11009,7 +11014,7 @@ with narrow binding events such as transcription factor ChIP-seq.") ("cutadapt" ,cutadapt))) (native-inputs `(("unzip" ,unzip))) - (home-page "http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/") + (home-page "https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/") (synopsis "Wrapper around Cutadapt and FastQC") (description "Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to @@ -11071,7 +11076,7 @@ matplotlib.use('Agg') ("python2-numpy" ,python2-numpy) ("python2-networkx" ,python2-networkx) ("python2-biopython" ,python2-biopython))) - (home-page "http://compbio.uthscsa.edu/GESS_Web/") + (home-page "https://compbio.uthscsa.edu/GESS_Web/") (synopsis "Detect exon-skipping events from raw RNA-seq data") (description "GESS is an implementation of a novel computational method to detect de @@ -11322,8 +11327,8 @@ models. TADbit is complemented by TADkit for visualizing 3D models.") ("libpng" ,libpng) ("mariadb" ,mariadb "lib") ("mariadb-dev" ,mariadb "dev") - ("openssl" ,openssl))) - (home-page "http://genome.cse.ucsc.edu/index.html") + ("openssl" ,openssl-1.0))) + (home-page "https://genome.cse.ucsc.edu/index.html") (synopsis "Assorted bioinformatics utilities") (description "This package provides the kentUtils, a selection of bioinformatics utilities used in combination with the UCSC genome @@ -11483,7 +11488,7 @@ Browser.") (sha256 (base32 "138mwsr4nf5qif4mrxx286mpnagxd1xwl6k8aidrjgknaqg88zyr")))) ("uglify-js" ,uglify-js))) - (home-page "http://www.bioinformatics.babraham.ac.uk/projects/bismark/") + (home-page "https://www.bioinformatics.babraham.ac.uk/projects/bismark/") (synopsis "Map bisulfite treated sequence reads and analyze methylation") (description "Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. @@ -11586,7 +11591,7 @@ using nucleotide or amino-acid sequence data.") `(("hdf5" ,hdf5) ("htslib" ,htslib) ("zlib" ,zlib))) - (home-page "http://pachterlab.github.io/kallisto/") + (home-page "https://pachterlab.github.io/kallisto/") (synopsis "Near-optimal RNA-Seq quantification") (description "Kallisto is a program for quantifying abundances of transcripts from @@ -11761,7 +11766,7 @@ dependency like SeqAn.") ("zlib" ,zlib))) (native-inputs `(("pkg-config" ,pkg-config))) - (home-page "http://www.cs.cmu.edu/~ckingsf/software/sailfish") + (home-page "https://www.cs.cmu.edu/~ckingsf/software/sailfish/") (synopsis "Mapping-based isoform quantification from RNA-Seq reads") (description "Sailfish is a tool for genomic transcript quantification from RNA-seq data. It requires a set of target transcripts (either from a @@ -13564,7 +13569,7 @@ such as Hi-C contact matrices.") ("python-six" ,python-six) ("python-tables" ,python-tables) ("python-unidecode" ,python-unidecode))) - (home-page "http://hicexplorer.readthedocs.io") + (home-page "https://hicexplorer.readthedocs.io") (synopsis "Process, analyze and visualize Hi-C data") (description "HiCExplorer is a powerful and easy to use set of tools to process, @@ -14646,7 +14651,7 @@ to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.") - (home-page "http://matsen.fhcrc.org/pplacer") + (home-page "https://matsen.fhcrc.org/pplacer/") (license license:gpl3)))) ;; This package is installed alongside 'pplacer'. It is a separate package so @@ -14702,14 +14707,14 @@ downstream analysis.") (build-system python-build-system) (arguments `(#:python ,python-2 - #:tests? #f)) ; some tests are interactive + #:tests? #f)) ; some tests are interactive (propagated-inputs `(("python-dendropy" ,python2-dendropy) ("python-matplotlib" ,python2-matplotlib) ("python-numpy" ,python2-numpy) ("python-pysam" ,python2-pysam) ("python-scipy" ,python2-scipy))) - (home-page "http://pypi.python.org/pypi/checkm/") + (home-page "https://pypi.org/project/Checkm/") (synopsis "Assess the quality of putative genome bins") (description "CheckM provides a set of tools for assessing the quality of genomes @@ -15361,7 +15366,7 @@ pairs.") ("r-rsamtools" ,r-rsamtools) ("r-edger" ,r-edger) ("r-igraph" ,r-igraph))) - (home-page "http://velocyto.org") + (home-page "https://velocyto.org") (synopsis "RNA velocity estimation in R") (description "This package provides basic routines for estimation of gene-specific |