09/09: gnu: Use HTTPS for (gnu packages bioinformatics) home pages.

[guix-commits]

nckx pushed a commit to branch master
in repository guix.

commit a19fb6a43648f6a3556d8139794ebd8646e792b8
Author: Tobias Geerinckx-Rice <address@hidden>
AuthorDate: Tue Jan 21 01:59:49 2020 +0100

    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.
---
 gnu/packages/bioinformatics.scm | 58 ++++++++++++++++++++---------------------
 1 file changed, 29 insertions(+), 29 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8454b3e..e8dac2a 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