diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 46 |
1 files changed, 23 insertions, 23 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9470e6eb1a..b5d132749f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1576,7 +1576,7 @@ use-case, we encourage users to compose functions to achieve their goals.") python-scipy)) (native-inputs (list python-cython python-pytest python-pytest-cov python-nose)) - (home-page "http://www.biom-format.org") + (home-page "https://www.biom-format.org") (synopsis "Biological Observation Matrix (BIOM) format utilities") (description "The BIOM file format is designed to be a general-use format for @@ -2503,7 +2503,7 @@ errors at the end of reads.") ("python" ,python-wrapper))) (native-inputs (list perl perl-clone perl-test-deep perl-test-simple)) - (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml") + (home-page "https://bowtie-bio.sourceforge.net/bowtie2/index.shtml") (synopsis "Fast and sensitive nucleotide sequence read aligner") (description "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing @@ -2545,7 +2545,7 @@ gapped, local, and paired-end alignment modes.") (inputs (list python-wrapper tbb-2020 zlib)) (supported-systems '("x86_64-linux")) - (home-page "http://bowtie-bio.sourceforge.net/index.shtml") + (home-page "https://bowtie-bio.sourceforge.net/index.shtml") (synopsis "Fast aligner for short nucleotide sequence reads") (description "Bowtie is a fast, memory-efficient short read aligner. It aligns short @@ -2666,7 +2666,7 @@ splice junctions between exons.") ;; Non-portable SSE instructions are used so building fails on platforms ;; other than x86_64. (supported-systems '("x86_64-linux")) - (home-page "http://bio-bwa.sourceforge.net/") + (home-page "https://bio-bwa.sourceforge.net/") (synopsis "Burrows-Wheeler sequence aligner") (description "BWA is a software package for mapping low-divergent sequences against a @@ -3259,7 +3259,7 @@ time.") zlib)) (native-inputs (list python-cython python-nose)) - (home-page "http://crossmap.sourceforge.net/") + (home-page "https://crossmap.sourceforge.net/") (synopsis "Convert genome coordinates between assemblies") (description "CrossMap is a program for conversion of genome coordinates or annotation @@ -4883,7 +4883,7 @@ high-throughput sequencing (HTS) assays") ("java-xz" ,java-xz))) (native-inputs (list java-testng)) - (home-page "http://samtools.github.io/htsjdk/") + (home-page "https://samtools.github.io/htsjdk/") (synopsis "Java API for high-throughput sequencing data (HTS) formats") (description "HTSJDK is an implementation of a unified Java library for accessing @@ -4926,7 +4926,7 @@ manipulating HTS data.") ("java-xz" ,java-xz))) (native-inputs (list java-junit)) - (home-page "http://samtools.github.io/htsjdk/") + (home-page "https://samtools.github.io/htsjdk/") (synopsis "Java API for high-throughput sequencing data (HTS) formats") (description "HTSJDK is an implementation of a unified Java library for accessing @@ -5031,7 +5031,7 @@ manipulating HTS data.") (list java-htsjdk java-guava)) (native-inputs (list java-testng)) - (home-page "http://broadinstitute.github.io/picard/") + (home-page "https://broadinstitute.github.io/picard/") (synopsis "Tools for manipulating high-throughput sequencing data and formats") (description "Picard is a set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats. Picard is implemented @@ -5120,7 +5120,7 @@ Class-Path: /~a \ (list java-htsjdk-2.10.1)) (native-inputs (list java-testng java-guava)) - (home-page "http://broadinstitute.github.io/picard/") + (home-page "https://broadinstitute.github.io/picard/") (synopsis "Tools for manipulating high-throughput sequencing data and formats") (description "Picard is a set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats. Picard is implemented @@ -5719,7 +5719,7 @@ data.") tar wget zlib)) - (home-page "http://kaiju.binf.ku.dk/") + (home-page "https://kaiju.binf.ku.dk/") (synopsis "Fast and sensitive taxonomic classification for metagenomics") (description "Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing @@ -6235,7 +6235,7 @@ predicts the locations of structural units in the sequences.") ("openblas" ,openblas))) (native-inputs (list which)) - (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho") + (home-page "https://www.bioinf.uni-leipzig.de/Software/proteinortho") (synopsis "Detect orthologous genes across species") (description "Proteinortho is a tool to detect orthologous genes across different @@ -6510,7 +6510,7 @@ phylogenies.") "rsem-run-prsem-testing-procedure")))))))) (inputs (list boost r-minimal perl htslib-1.3 zlib)) - (home-page "http://deweylab.biostat.wisc.edu/rsem/") + (home-page "https://deweylab.biostat.wisc.edu/rsem/") (synopsis "Estimate gene expression levels from RNA-Seq data") (description "RSEM is a software package for estimating gene and isoform expression @@ -6545,7 +6545,7 @@ BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.") zlib)) (native-inputs (list python-nose)) - (home-page "http://rseqc.sourceforge.net/") + (home-page "https://rseqc.sourceforge.net/") (synopsis "RNA-seq quality control package") (description "RSeQC provides a number of modules that can comprehensively evaluate @@ -6605,7 +6605,7 @@ distribution, coverage uniformity, strand specificity, etc.") ("readline" ,readline))) (native-inputs (list pkg-config)) - (home-page "http://seek.princeton.edu") + (home-page "https://seek.princeton.edu") (synopsis "Gene co-expression search engine") (description "SEEK is a computational gene co-expression search engine. SEEK provides @@ -6646,7 +6646,7 @@ to the user's query of interest.") (native-inputs (list pkg-config)) (inputs (list htslib ncurses perl python zlib)) - (home-page "http://samtools.sourceforge.net") + (home-page "https://samtools.sourceforge.net") (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments") (description "Samtools implements various utilities for post-processing nucleotide @@ -7724,7 +7724,7 @@ optionally compressed by gzip.") (install-file "SNAPCommand" bin))))))) (native-inputs (list zlib)) - (home-page "http://snap.cs.berkeley.edu/") + (home-page "https://snap.cs.berkeley.edu/") (synopsis "Short read DNA sequence aligner") (description "SNAP is a fast and accurate aligner for short DNA reads. It is @@ -7991,7 +7991,7 @@ sequences.") ;; no "configure" script (delete 'configure)))) (inputs (list zlib)) - (home-page "http://subread.sourceforge.net/") + (home-page "https://subread.sourceforge.net/") (synopsis "Tool kit for processing next-gen sequencing data") (description "The subread package contains the following tools: subread aligner, a @@ -8038,7 +8038,7 @@ against local background noises.") (install-file "stringtie" bin))))))) (inputs (list bzip2 htslib-for-stringtie libdeflate zlib)) - (home-page "http://ccb.jhu.edu/software/stringtie/") + (home-page "https://ccb.jhu.edu/software/stringtie/") (synopsis "Transcript assembly and quantification for RNA-Seq data") (description "StringTie is a fast and efficient assembler of RNA-Seq sequence @@ -9152,7 +9152,7 @@ of contact distributions around selected landmarks.") (base32 "1hsx6qgwr0i67fhy9257zj7s0ppncph2hjgbia5nn6nfmj0ax6l9")))) (build-system r-build-system) - (home-page "http://centipede.uchicago.edu/") + (home-page "https://centipede.uchicago.edu/") (synopsis "Predict transcription factor binding sites") (description "CENTIPEDE applies a hierarchical Bayesian mixture model to infer regions @@ -9390,7 +9390,7 @@ experience substantial biological insertions and deletions.") perl-getopt-long perl-json perl-statistics-pca)) - (home-page "http://prinseq.sourceforge.net/") + (home-page "https://prinseq.sourceforge.net/") (synopsis "Preprocess sequence data in FASTA or FASTQ formats") (description "PRINSEQ is a bioinformatics tool to help you preprocess your genomic or @@ -9875,7 +9875,7 @@ AM_CONDITIONAL(AMPNG, true)")) zlib)) (native-inputs (list autoconf automake libtool pkg-config)) - (home-page "http://emboss.sourceforge.net") + (home-page "https://emboss.sourceforge.net") (synopsis "Molecular biology analysis suite") (description "EMBOSS is the \"European Molecular Biology Open Software Suite\". EMBOSS is an analysis package specially developed for the needs of @@ -10552,7 +10552,7 @@ remove biased methylation positions for RRBS sequence files.") (for-each (lambda (file) (install-file file target)) (find-files "../exe" ".*")))))))) - (home-page "http://evolution.genetics.washington.edu/phylip/") + (home-page "https://evolution.genetics.washington.edu/phylip/") (synopsis "Tools for inferring phylogenies") (description "PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees).") @@ -16831,7 +16831,7 @@ The output is in SAM format.") (list libxml2)) (native-inputs (list check swig)) - (home-page "http://sbml.org/Software/libSBML") + (home-page "https://sbml.org/Software/libSBML") (synopsis "Process SBML files and data streams") (description "LibSBML is a library to help you read, write, manipulate, translate, and validate SBML files and data streams. The @dfn{Systems Biology |