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gnu: Use HTTPS for (gnu packages bioinformatics) home pages. 

* gnu/packages/bioinformatics (bamm, ribodiff, python-biopython)
(discrover, hisat, hisat2, htseq, fastqc, htslib, python2-pbcore, roary)
(sortmerna, r-qtl, multiqc, r-deseq, r-fastseg, sambamba, trim-galore)
(gess, kentutils, bismark, kallisto, sailfish, python-hicexplorer)
(pplacer, python2-checkm-genome, r-velocyto)[home-page]: Use HTTPS.
master
Tobias Geerinckx-Rice 2020-01-21 01:59:49 +01:00
parent 72607005e4
commit a19fb6a436
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1 changed files with 29 additions and 29 deletions
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@ -261,7 +261,7 @@ structure of the predicted RNA.")
("coreutils" ,coreutils))) ("coreutils" ,coreutils)))
(propagated-inputs (propagated-inputs
`(("python-numpy" ,python2-numpy))) `(("python-numpy" ,python2-numpy)))
(home-page "http://ecogenomics.github.io/BamM/") (home-page "https://ecogenomics.github.io/BamM/")
(synopsis "Metagenomics-focused BAM file manipulator") (synopsis "Metagenomics-focused BAM file manipulator")
(description (description
"BamM is a C library, wrapped in python, to efficiently generate and "BamM is a C library, wrapped in python, to efficiently generate and
@ -726,7 +726,7 @@ provides the Ribotaper pipeline.")
(native-inputs (native-inputs
`(("python-mock" ,python2-mock) `(("python-mock" ,python2-mock)
("python-nose" ,python2-nose))) ("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") (synopsis "Detect translation efficiency changes from ribosome footprints")
(description "RiboDiff is a statistical tool that detects the protein (description "RiboDiff is a statistical tool that detects the protein
translational efficiency change from Ribo-Seq (ribosome footprinting) and 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))))) (lambda _ (setenv "HOME" "/tmp") #t)))))
(propagated-inputs (propagated-inputs
`(("python-numpy" ,python-numpy))) `(("python-numpy" ,python-numpy)))
(home-page "http://biopython.org/") (home-page "https://biopython.org/")
(synopsis "Tools for biological computation in Python") (synopsis "Tools for biological computation in Python")
(description (description
"Biopython is a set of tools for biological computation including parsers "Biopython is a set of tools for biological computation including parsers
@ -2676,7 +2676,7 @@ data and settings.")
texlive-latex-pgf ; tikz texlive-latex-pgf ; tikz
texlive-latex-verbatimbox))) texlive-latex-verbatimbox)))
("imagemagick" ,imagemagick))) ("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") (synopsis "Discover discriminative nucleotide sequence motifs")
(description "Discrover is a motif discovery method to find binding sites (description "Discrover is a motif discovery method to find binding sites
of nucleic acid binding proteins.") of nucleic acid binding proteins.")
@ -3381,7 +3381,7 @@ estimates transcript expression.")
;; Non-portable SSE instructions are used so building fails on platforms ;; Non-portable SSE instructions are used so building fails on platforms
;; other than x86_64. ;; other than x86_64.
(supported-systems '("x86_64-linux")) (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") (synopsis "Hierarchical indexing for spliced alignment of transcripts")
(description (description
"HISAT is a fast and sensitive spliced alignment program for mapping "HISAT is a fast and sensitive spliced alignment program for mapping
@ -3435,7 +3435,7 @@ particular, reads spanning multiple exons.")
`(("unzip" ,unzip) ; needed for archive from ftp `(("unzip" ,unzip) ; needed for archive from ftp
("perl" ,perl) ("perl" ,perl)
("pandoc" ,ghc-pandoc))) ; for documentation ("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") (synopsis "Graph-based alignment of genomic sequencing reads")
(description "HISAT2 is a fast and sensitive alignment program for mapping (description "HISAT2 is a fast and sensitive alignment program for mapping
next-generation sequencing reads (both DNA and RNA) to a population of human next-generation sequencing reads (both DNA and RNA) to a population of human
@ -3495,7 +3495,7 @@ HMMs).")
(inputs (inputs
`(("python-pysam" ,python-pysam) `(("python-pysam" ,python-pysam)
("python-matplotlib" ,python-matplotlib))) ("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") (synopsis "Analysing high-throughput sequencing data with Python")
(description (description
"HTSeq is a Python package that provides infrastructure to process data "HTSeq is a Python package that provides infrastructure to process data
@ -3970,7 +3970,7 @@ VCF.")
("java-jbzip2" ,java-jbzip2))) ("java-jbzip2" ,java-jbzip2)))
(native-inputs (native-inputs
`(("unzip" ,unzip))) `(("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") (synopsis "Quality control tool for high throughput sequence data")
(description (description
"FastQC aims to provide a simple way to do some quality control "FastQC aims to provide a simple way to do some quality control
@ -4049,7 +4049,7 @@ performance.")
`(("zlib" ,zlib))) `(("zlib" ,zlib)))
(native-inputs (native-inputs
`(("perl" ,perl))) `(("perl" ,perl)))
(home-page "http://www.htslib.org") (home-page "https://www.htslib.org")
(synopsis "C library for reading/writing high-throughput sequencing data") (synopsis "C library for reading/writing high-throughput sequencing data")
(description (description
"HTSlib is a C library for reading/writing high-throughput sequencing "HTSlib is a C library for reading/writing high-throughput sequencing
@ -4743,7 +4743,7 @@ interrupted by stop codons. OrfM finds and prints these ORFs.")
`(("python-nose" ,python2-nose) `(("python-nose" ,python2-nose)
("python-sphinx" ,python2-sphinx) ("python-sphinx" ,python2-sphinx)
("python-pyxb" ,python2-pyxb))) ("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") (synopsis "Library for reading and writing PacBio data files")
(description (description
"The pbcore package provides Python APIs for interacting with PacBio data "The pbcore package provides Python APIs for interacting with PacBio data
@ -5127,7 +5127,7 @@ partial genes, and identifies translation initiation sites.")
("r-minimal" ,r-minimal) ("r-minimal" ,r-minimal)
("r-ggplot2" ,r-ggplot2) ("r-ggplot2" ,r-ggplot2)
("coreutils" ,coreutils))) ("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") (synopsis "High speed stand-alone pan genome pipeline")
(description (description
"Roary is a high speed stand alone pan genome pipeline, which takes "Roary is a high speed stand alone pan genome pipeline, which takes
@ -6269,7 +6269,7 @@ of these reads to align data quickly through a hash-based indexing scheme.")
#t)))))) #t))))))
(inputs (inputs
`(("zlib" ,zlib))) `(("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") (synopsis "Biological sequence analysis tool for NGS reads")
(description (description
"SortMeRNA is a biological sequence analysis tool for filtering, mapping "SortMeRNA is a biological sequence analysis tool for filtering, mapping
@ -8237,7 +8237,7 @@ throughput genetic sequencing data sets using regression methods.")
(base32 (base32
"03lmvydln8b7666b6w46qbryhf83vsd11d4y2v95rfgvqgq66l1i")))) "03lmvydln8b7666b6w46qbryhf83vsd11d4y2v95rfgvqgq66l1i"))))
(build-system r-build-system) (build-system r-build-system)
(home-page "http://rqtl.org/") (home-page "https://rqtl.org/")
(synopsis "R package for analyzing QTL experiments in genetics") (synopsis "R package for analyzing QTL experiments in genetics")
(description "R/qtl is an extension library for the R statistics (description "R/qtl is an extension library for the R statistics
system. It is used to analyze experimental crosses for identifying system. It is used to analyze experimental crosses for identifying
@ -8313,7 +8313,7 @@ libraries for systems that do not have these available via other means.")
(propagated-inputs (propagated-inputs
`(("r-optparse" ,r-optparse) `(("r-optparse" ,r-optparse)
("r-rcolorbrewer" ,r-rcolorbrewer))) ("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") (synopsis "Analysis framework for RNA secondary structure")
(description (description
"The R4RNA package aims to be a general framework for the analysis of RNA "The R4RNA package aims to be a general framework for the analysis of RNA
@ -8933,7 +8933,7 @@ replacement for strverscmp.")
(("['\"]matplotlib.*?['\"]") (("['\"]matplotlib.*?['\"]")
"'matplotlib'")) "'matplotlib'"))
#t))))) #t)))))
(home-page "http://multiqc.info") (home-page "https://multiqc.info")
(synopsis "Aggregate bioinformatics analysis reports") (synopsis "Aggregate bioinformatics analysis reports")
(description (description
"MultiQC is a tool to aggregate bioinformatics results across many "MultiQC is a tool to aggregate bioinformatics results across many
@ -9603,7 +9603,7 @@ classes.")
("r-locfit" ,r-locfit) ("r-locfit" ,r-locfit)
("r-mass" ,r-mass) ("r-mass" ,r-mass)
("r-rcolorbrewer" ,r-rcolorbrewer))) ("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") (synopsis "Differential gene expression analysis")
(description (description
"This package provides tools for estimating variance-mean dependence in "This package provides tools for estimating variance-mean dependence in
@ -9732,7 +9732,7 @@ by the user, helping with quick and reproducible access.")
("r-genomicranges" ,r-genomicranges) ("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges) ("r-iranges" ,r-iranges)
("r-s4vectors" ,r-s4vectors))) ("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") (synopsis "Fast segmentation algorithm for genetic sequencing data")
(description (description
"Fastseg implements a very fast and efficient segmentation algorithm. "Fastseg implements a very fast and efficient segmentation algorithm.
@ -10897,7 +10897,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.")
(inputs (inputs
`(("lz4" ,lz4) `(("lz4" ,lz4)
("htslib" ,htslib-for-sambamba))) ("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") (synopsis "Tools for working with SAM/BAM data")
(description "Sambamba is a high performance modern robust and (description "Sambamba is a high performance modern robust and
fast tool (and library), written in the D programming language, for fast tool (and library), written in the D programming language, for
@ -11014,7 +11014,7 @@ with narrow binding events such as transcription factor ChIP-seq.")
("cutadapt" ,cutadapt))) ("cutadapt" ,cutadapt)))
(native-inputs (native-inputs
`(("unzip" ,unzip))) `(("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") (synopsis "Wrapper around Cutadapt and FastQC")
(description "Trim Galore! is a wrapper script to automate quality and (description "Trim Galore! is a wrapper script to automate quality and
adapter trimming as well as quality control, with some added functionality to adapter trimming as well as quality control, with some added functionality to
@ -11076,7 +11076,7 @@ matplotlib.use('Agg')
("python2-numpy" ,python2-numpy) ("python2-numpy" ,python2-numpy)
("python2-networkx" ,python2-networkx) ("python2-networkx" ,python2-networkx)
("python2-biopython" ,python2-biopython))) ("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") (synopsis "Detect exon-skipping events from raw RNA-seq data")
(description (description
"GESS is an implementation of a novel computational method to detect de "GESS is an implementation of a novel computational method to detect de
@ -11328,7 +11328,7 @@ models. TADbit is complemented by TADkit for visualizing 3D models.")
("mariadb" ,mariadb "lib") ("mariadb" ,mariadb "lib")
("mariadb-dev" ,mariadb "dev") ("mariadb-dev" ,mariadb "dev")
("openssl" ,openssl-1.0))) ("openssl" ,openssl-1.0)))
(home-page "http://genome.cse.ucsc.edu/index.html") (home-page "https://genome.cse.ucsc.edu/index.html")
(synopsis "Assorted bioinformatics utilities") (synopsis "Assorted bioinformatics utilities")
(description "This package provides the kentUtils, a selection of (description "This package provides the kentUtils, a selection of
bioinformatics utilities used in combination with the UCSC genome bioinformatics utilities used in combination with the UCSC genome
@ -11488,7 +11488,7 @@ Browser.")
(sha256 (sha256
(base32 "138mwsr4nf5qif4mrxx286mpnagxd1xwl6k8aidrjgknaqg88zyr")))) (base32 "138mwsr4nf5qif4mrxx286mpnagxd1xwl6k8aidrjgknaqg88zyr"))))
("uglify-js" ,uglify-js))) ("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") (synopsis "Map bisulfite treated sequence reads and analyze methylation")
(description "Bismark is a program to map bisulfite treated sequencing (description "Bismark is a program to map bisulfite treated sequencing
reads to a genome of interest and perform methylation calls in a single step. reads to a genome of interest and perform methylation calls in a single step.
@ -11591,7 +11591,7 @@ using nucleotide or amino-acid sequence data.")
`(("hdf5" ,hdf5) `(("hdf5" ,hdf5)
("htslib" ,htslib) ("htslib" ,htslib)
("zlib" ,zlib))) ("zlib" ,zlib)))
(home-page "http://pachterlab.github.io/kallisto/") (home-page "https://pachterlab.github.io/kallisto/")
(synopsis "Near-optimal RNA-Seq quantification") (synopsis "Near-optimal RNA-Seq quantification")
(description (description
"Kallisto is a program for quantifying abundances of transcripts from "Kallisto is a program for quantifying abundances of transcripts from
@ -11766,7 +11766,7 @@ dependency like SeqAn.")
("zlib" ,zlib))) ("zlib" ,zlib)))
(native-inputs (native-inputs
`(("pkg-config" ,pkg-config))) `(("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") (synopsis "Mapping-based isoform quantification from RNA-Seq reads")
(description "Sailfish is a tool for genomic transcript quantification (description "Sailfish is a tool for genomic transcript quantification
from RNA-seq data. It requires a set of target transcripts (either from a from RNA-seq data. It requires a set of target transcripts (either from a
@ -13569,7 +13569,7 @@ such as Hi-C contact matrices.")
("python-six" ,python-six) ("python-six" ,python-six)
("python-tables" ,python-tables) ("python-tables" ,python-tables)
("python-unidecode" ,python-unidecode))) ("python-unidecode" ,python-unidecode)))
(home-page "http://hicexplorer.readthedocs.io") (home-page "https://hicexplorer.readthedocs.io")
(synopsis "Process, analyze and visualize Hi-C data") (synopsis "Process, analyze and visualize Hi-C data")
(description (description
"HiCExplorer is a powerful and easy to use set of tools to process, "HiCExplorer is a powerful and easy to use set of tools to process,
@ -14651,7 +14651,7 @@ to maximize phylogenetic likelihood or posterior probability according to a
reference alignment. Pplacer is designed to be fast, to give useful reference alignment. Pplacer is designed to be fast, to give useful
information about uncertainty, and to offer advanced visualization and information about uncertainty, and to offer advanced visualization and
downstream analysis.") downstream analysis.")
(home-page "http://matsen.fhcrc.org/pplacer") (home-page "https://matsen.fhcrc.org/pplacer/")
(license license:gpl3)))) (license license:gpl3))))
;; This package is installed alongside 'pplacer'. It is a separate package so ;; This package is installed alongside 'pplacer'. It is a separate package so
@ -14707,14 +14707,14 @@ downstream analysis.")
(build-system python-build-system) (build-system python-build-system)
(arguments (arguments
`(#:python ,python-2 `(#:python ,python-2
#:tests? #f)) ; some tests are interactive #:tests? #f)) ; some tests are interactive
(propagated-inputs (propagated-inputs
`(("python-dendropy" ,python2-dendropy) `(("python-dendropy" ,python2-dendropy)
("python-matplotlib" ,python2-matplotlib) ("python-matplotlib" ,python2-matplotlib)
("python-numpy" ,python2-numpy) ("python-numpy" ,python2-numpy)
("python-pysam" ,python2-pysam) ("python-pysam" ,python2-pysam)
("python-scipy" ,python2-scipy))) ("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") (synopsis "Assess the quality of putative genome bins")
(description (description
"CheckM provides a set of tools for assessing the quality of genomes "CheckM provides a set of tools for assessing the quality of genomes
@ -15366,7 +15366,7 @@ pairs.")
("r-rsamtools" ,r-rsamtools) ("r-rsamtools" ,r-rsamtools)
("r-edger" ,r-edger) ("r-edger" ,r-edger)
("r-igraph" ,r-igraph))) ("r-igraph" ,r-igraph)))
(home-page "http://velocyto.org") (home-page "https://velocyto.org")
(synopsis "RNA velocity estimation in R") (synopsis "RNA velocity estimation in R")
(description (description
"This package provides basic routines for estimation of gene-specific "This package provides basic routines for estimation of gene-specific