diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 58 |
1 files changed, 29 insertions, 29 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8454b3e25c..e8dac2a12b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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 |