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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)))
(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
@ -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.")
@ -3381,7 +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
@ -3435,7 +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
@ -3495,7 +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
@ -3970,7 +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
@ -4049,7 +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
@ -4743,7 +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
@ -5127,7 +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
@ -6269,7 +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
@ -8237,7 +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
@ -8313,7 +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
@ -8933,7 +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
@ -9603,7 +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
@ -9732,7 +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.
@ -10897,7 +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
@ -11014,7 +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
@ -11076,7 +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
@ -11328,7 +11328,7 @@ models. TADbit is complemented by TADkit for visualizing 3D models.")
("mariadb" ,mariadb "lib")
("mariadb-dev" ,mariadb "dev")
("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")
(description "This package provides the kentUtils, a selection of
bioinformatics utilities used in combination with the UCSC genome
@ -11488,7 +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.
@ -11591,7 +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
@ -11766,7 +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
@ -13569,7 +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,
@ -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
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
@ -14707,14 +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
@ -15366,7 +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