;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
+;;; Copyright © 2020 Pierre Langlois <pierre.langlois@gmx.com>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (guix build-system ruby)
#:use-module (guix build-system scons)
#:use-module (guix build-system trivial)
+ #:use-module (guix deprecation)
#:use-module (gnu packages)
#:use-module (gnu packages autotools)
#:use-module (gnu packages algebra)
(method git-fetch)
;; BamM is not available on pypi.
(uri (git-reference
- (url "https://github.com/Ecogenomics/BamM.git")
+ (url "https://github.com/Ecogenomics/BamM")
(commit version)
(recursive? #t)))
(file-name (git-file-name name version))
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/pezmaster31/bamtools.git")
+ (url "https://github.com/pezmaster31/bamtools")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/bedops/bedops.git")
+ (url "https://github.com/bedops/bedops")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/PacificBiosciences/pbbam.git")
+ (url "https://github.com/PacificBiosciences/pbbam")
(commit version)))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/PacificBiosciences/blasr_libcpp.git")
+ (url "https://github.com/PacificBiosciences/blasr_libcpp")
(commit version)))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/PacificBiosciences/blasr.git")
+ (url "https://github.com/PacificBiosciences/blasr")
(commit version)))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ratschlab/RiboDiff.git")
+ (url "https://github.com/ratschlab/RiboDiff")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/lh3/bioawk.git")
+ (url "https://github.com/lh3/bioawk")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
;; Use GitHub as source because PyPI distribution does not contain
;; test data: https://github.com/biocore/biom-format/issues/693
(uri (git-reference
- (url "https://github.com/biocore/biom-format.git")
+ (url "https://github.com/biocore/biom-format")
(commit version)))
(file-name (git-file-name name version))
(sha256
("python-future" ,python-future)
("python-click" ,python-click)
("python-h5py" ,python-h5py)
- ("python-pandas" ,python-pandas)))
+ ;; FIXME: Upgrade to pandas 1.0 when
+ ;; https://github.com/biocore/biom-format/issues/837 is resolved.
+ ("python-pandas" ,python-pandas-0.25)))
(native-inputs
`(("python-cython" ,python-cython)
("python-pytest" ,python-pytest)
(define-public blast+
(package
(name "blast+")
- (version "2.7.1")
+ (version "2.10.1")
(source (origin
(method url-fetch)
(uri (string-append
- "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/"
+ "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/"
version "/ncbi-blast-" version "+-src.tar.gz"))
(sha256
(base32
- "1jlq0afxxgczpp35k6mxh8mn4jzq7vqcnaixk166sfj10wq8v9qh"))
+ "11kvrrl0mcwww6530r55hccpg3x3msmhr3051fwnjbq8rzg2j1qi"))
(modules '((guix build utils)))
(snippet
'(begin
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/BenLangmead/bowtie2.git")
+ (url "https://github.com/BenLangmead/bowtie2")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(modify-phases %standard-phases
(delete 'configure))))
(inputs
- `(("tbb" ,tbb)
+ `(("python-wrapper" ,python-wrapper)
+ ("tbb" ,tbb)
("zlib" ,zlib)))
(supported-systems '("x86_64-linux"))
(home-page "http://bowtie-bio.sourceforge.net/index.shtml")
'(#:parallel-build? #f ; not supported
#:phases
(modify-phases %standard-phases
+ (add-after 'set-paths 'hide-default-gcc
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((gcc (assoc-ref inputs "gcc")))
+ ;; Remove the default GCC from CPLUS_INCLUDE_PATH to prevent
+ ;; conflicts with the GCC 5 input.
+ (setenv "CPLUS_INCLUDE_PATH"
+ (string-join
+ (delete (string-append gcc "/include/c++")
+ (string-split (getenv "CPLUS_INCLUDE_PATH") #\:))
+ ":"))
+ #t)))
(add-after 'unpack 'use-system-samtools
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "src/Makefile.in"
(("#include <sam.h>") "#include <samtools/sam.h>"))
#t)))))
(native-inputs
- `(("gcc" ,gcc-5))) ;; doesn't build with later versions
+ `(("gcc@5" ,gcc-5))) ;; doesn't build with later versions
(inputs
`(("boost" ,boost)
("bowtie" ,bowtie)
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/pkerpedjiev/bwa-pssm.git")
+ (url "https://github.com/pkerpedjiev/bwa-pssm")
(commit version)))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/brentp/bwa-meth.git")
+ (url "https://github.com/brentp/bwa-meth")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(method git-fetch)
;; Test data is missing on PyPi.
(uri (git-reference
- (url "https://github.com/pysam-developers/pysam.git")
+ (url "https://github.com/pysam-developers/pysam")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/mhammell-laboratory/tetoolkit.git")
+ (url "https://github.com/mhammell-laboratory/tetoolkit")
(commit version)))
(file-name (git-file-name name version))
(sha256
(define-public clipper
(package
(name "clipper")
- (version "1.2.1")
+ (version "2.0")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/YeoLab/clipper.git")
+ (url "https://github.com/YeoLab/clipper")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
- "0fja1rj84wp9vpj8rxpj3n8zqzcqq454m904yp9as1w4phccirjb"))
- (modules '((guix build utils)))
- (snippet
- '(begin
- ;; remove unnecessary setup dependency
- (substitute* "setup.py"
- (("setup_requires = .*") ""))
- #t))))
+ "1bcag4lb5bkzsj2vg7lrq24aw6yfgq275ifrbhd82l7kqgbbjbkv"))))
(build-system python-build-system)
(arguments
- `(#:python ,python-2 ; only Python 2 is supported
- #:phases
+ `(#:phases
(modify-phases %standard-phases
- ;; This is fixed in upstream commit
- ;; f6c2990198f906bf97730d95695b4bd5a6d01ddb.
- (add-after 'unpack 'fix-typo
- (lambda _
- (substitute* "clipper/src/readsToWiggle.pyx"
- (("^sc.*") ""))
- #t)))))
+ (add-before 'reset-gzip-timestamps 'make-files-writable
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; Make sure .gz files are writable so that the
+ ;; 'reset-gzip-timestamps' phase can do its work.
+ (let ((out (assoc-ref outputs "out")))
+ (for-each make-file-writable
+ (find-files out "\\.gz$"))
+ #t))))))
(inputs
- `(("htseq" ,python2-htseq)
- ("python-pybedtools" ,python2-pybedtools)
- ("python-cython" ,python2-cython)
- ("python-scikit-learn" ,python2-scikit-learn)
- ("python-matplotlib" ,python2-matplotlib)
- ("python-pandas" ,python2-pandas)
- ("python-pysam" ,python2-pysam)
- ("python-numpy" ,python2-numpy)
- ("python-scipy" ,python2-scipy)))
+ `(("htseq" ,htseq)
+ ("python-pybedtools" ,python-pybedtools)
+ ("python-cython" ,python-cython)
+ ("python-scikit-learn" ,python-scikit-learn)
+ ("python-matplotlib" ,python-matplotlib)
+ ("python-pandas" ,python-pandas)
+ ("python-pysam" ,python-pysam)
+ ("python-numpy" ,python-numpy)
+ ("python-scipy" ,python-scipy)))
(native-inputs
- `(("python-mock" ,python2-mock) ; for tests
- ("python-nose" ,python2-nose) ; for tests
- ("python-pytz" ,python2-pytz))) ; for tests
+ `(("python-setuptools-git" ,python-setuptools-git)
+ ("python-mock" ,python-mock) ; for tests
+ ("python-nose" ,python-nose) ; for tests
+ ("python-pytz" ,python-pytz))) ; for tests
(home-page "https://github.com/YeoLab/clipper")
(synopsis "CLIP peak enrichment recognition")
(description
(name "python-deeptools")
(version "3.4.3")
(source (origin
- (method url-fetch)
- (uri (pypi-uri "deepTools" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/deeptools/deepTools")
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "1azgjniss5ff6a90nicdjkxyjwqmi3gzfn09gra42hwlz19hipxb"))))
+ "0l09vyynz6s6w7fnyd94rpys4a6aja6kp4gli64pngdxdz3md1nl"))))
(build-system python-build-system)
+ (native-inputs
+ `(("python-mock" ,python-mock)
+ ("python-nose" ,python-nose)))
(propagated-inputs
`(("python-matplotlib" ,python-matplotlib)
("python-numpy" ,python-numpy)
("python-pysam" ,python-pysam)
("python-scipy" ,python-scipy)
("python-deeptoolsintervals" ,python-deeptoolsintervals)
- ("python-plotly" ,python-plotly)))
+ ("python-plotly" ,python-plotly-2.4.1)))
(home-page "https://pypi.org/project/deepTools/")
(synopsis "Useful tools for exploring deep sequencing data")
(description "This package addresses the challenge of handling large amounts
;; remainder of the code is licensed under the MIT license.
(license (list license:bsd-3 license:expat))))
+(define-deprecated deeptools python-deeptools)
+
(define-public cutadapt
(package
(name "cutadapt")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/dpryan79/libBigWig.git")
+ (url "https://github.com/dpryan79/libBigWig")
(commit version)))
(file-name (git-file-name name version))
(sha256
(method git-fetch)
;; Source from GitHub so that tests are included.
(uri (git-reference
- (url "https://github.com/jeetsukumaran/DendroPy.git")
+ (url "https://github.com/jeetsukumaran/DendroPy")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
with Python.")
(license license:expat)))
-(define-public deeptools
- (package
- (name "deeptools")
- (version "3.1.3")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/deeptools/deepTools.git")
- (commit version)))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "1vggnf52g6q2vifdl4cyi7s2fnfqq0ky2zrkj5zv2qfzsc3p3siw"))))
- (build-system python-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- ;; This phase fails, but it's not needed.
- (delete 'reset-gzip-timestamps))))
- (inputs
- `(("python-plotly" ,python-plotly)
- ("python-scipy" ,python-scipy)
- ("python-numpy" ,python-numpy)
- ("python-numpydoc" ,python-numpydoc)
- ("python-matplotlib" ,python-matplotlib)
- ("python-pysam" ,python-pysam)
- ("python-py2bit" ,python-py2bit)
- ("python-pybigwig" ,python-pybigwig)))
- (native-inputs
- `(("python-mock" ,python-mock) ;for tests
- ("python-nose" ,python-nose) ;for tests
- ("python-pytz" ,python-pytz))) ;for tests
- (home-page "https://github.com/deeptools/deepTools")
- (synopsis "Tools for normalizing and visualizing deep-sequencing data")
- (description
- "DeepTools addresses the challenge of handling the large amounts of data
-that are now routinely generated from DNA sequencing centers. To do so,
-deepTools contains useful modules to process the mapped reads data to create
-coverage files in standard bedGraph and bigWig file formats. By doing so,
-deepTools allows the creation of normalized coverage files or the comparison
-between two files (for example, treatment and control). Finally, using such
-normalized and standardized files, multiple visualizations can be created to
-identify enrichments with functional annotations of the genome.")
- (license license:gpl3+)))
-
(define-public delly
(package
(name "delly")
- (version "0.7.9")
+ (version "0.8.3")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/dellytools/delly.git")
+ (url "https://github.com/dellytools/delly")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "034jqsxswy9gqdh2zkgc1js99qkv75ks4xvzgmh0284sraagv61z"))
+ (base32 "1ibnplgfzj96w8glkx17v7sld3pm402fr5ybmf3h0rlcryabxrqy"))
(modules '((guix build utils)))
(snippet
'(begin
#t))))))
(inputs
`(("boost" ,boost)
+ ("bzip2" ,bzip2)
("htslib" ,htslib)
- ("zlib" ,zlib)
- ("bzip2" ,bzip2)))
+ ("zlib" ,zlib)))
(home-page "https://github.com/dellytools/delly")
(synopsis "Integrated structural variant prediction method")
(description "Delly is an integrated structural variant prediction method
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/bbuchfink/diamond.git")
+ (url "https://github.com/bbuchfink/diamond")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/maaskola/discrover.git")
+ (url "https://github.com/maaskola/discrover")
(commit version)))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/DReichLab/EIG.git")
+ (url "https://github.com/DReichLab/EIG")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(define-public express
(package
(name "express")
- (version "1.5.1")
+ (version "1.5.3")
(source (origin
- (method url-fetch)
- (uri
- (string-append
- "http://bio.math.berkeley.edu/eXpress/downloads/express-"
- version "/express-" version "-src.tgz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/adarob/eXpress")
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "03rczxd0gjp2l1jxcmjfmf5j94j77zqyxa6x063zsc585nj40n0c"))))
+ "18nb22n7x820fzjngf4qgyb3mspqkw7xyk7v7s5ps6wfrd8qwscb"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ;no "check" target
(("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib")
(string-append (assoc-ref inputs "bamtools") "/lib"))
(("libprotobuf.a") "libprotobuf.so"))
+ #t))
+ (add-after 'unpack 'remove-update-check
+ (lambda _
+ (substitute* "src/main.cpp"
+ (("#include \"update_check.h\"") "")
+ (("check_version\\(PACKAGE_VERSION\\);") ""))
#t)))))
(inputs
`(("boost" ,boost)
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/dparks1134/ExpressBetaDiversity.git")
+ (url "https://github.com/dparks1134/ExpressBetaDiversity")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/seqan/flexbar.git")
+ (url "https://github.com/seqan/flexbar")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ctSkennerton/fxtract.git")
+ (url "https://github.com/ctSkennerton/fxtract")
(commit version)))
(file-name (git-file-name name version))
(sha256
,(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ctSkennerton/util.git")
+ (url "https://github.com/ctSkennerton/util")
(commit util-commit)))
(file-name (string-append
"ctstennerton-util-" util-commit "-checkout"))
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/xiangzhou/GEMMA.git")
+ (url "https://github.com/xiangzhou/GEMMA")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/nboley/grit.git")
+ (url "https://github.com/nboley/grit")
(commit version)))
(file-name (git-file-name name version))
(sha256
(native-inputs
`(("unzip" ,unzip) ; needed for archive from ftp
("perl" ,perl)
- ("pandoc" ,ghc-pandoc))) ; for documentation
+ ("pandoc" ,pandoc))) ; for documentation
(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
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/samtools/htsjdk.git")
+ (url "https://github.com/samtools/htsjdk")
(commit version)))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/samtools/htsjdk.git")
+ (url "https://github.com/samtools/htsjdk")
(commit version)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/samtools/htsjdk.git")
+ (url "https://github.com/samtools/htsjdk")
(commit version)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/broadinstitute/picard.git")
+ (url "https://github.com/broadinstitute/picard")
(commit version)))
(file-name (string-append "java-picard-" version "-checkout"))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/broadinstitute/picard.git")
+ (url "https://github.com/broadinstitute/picard")
(commit version)))
(file-name (string-append "java-picard-" version "-checkout"))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/broadinstitute/picard.git")
+ (url "https://github.com/broadinstitute/picard")
(commit version)))
(file-name (string-append "java-picard-" version "-checkout"))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/OpenGene/fastp.git")
+ (url "https://github.com/OpenGene/fastp")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/nboley/idr.git")
+ (url "https://github.com/nboley/idr")
(commit version)))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/dib-lab/khmer.git")
+ (url "https://github.com/dib-lab/khmer")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
;; The PyPi tarball does not contain tests.
(method git-fetch)
(uri (git-reference
- (url "https://github.com/taoliu/MACS.git")
+ (url "https://github.com/taoliu/MACS")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/marbl/mash.git")
+ (url "https://github.com/marbl/mash")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ctSkennerton/minced.git")
+ (url "https://github.com/ctSkennerton/minced")
(commit version)))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/tjunier/newick_utils.git")
+ (url "https://github.com/tjunier/newick_utils")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/PacificBiosciences/cDNA_primer.git")
+ (url "https://github.com/PacificBiosciences/cDNA_primer")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/hyattpd/Prodigal.git")
+ (url "https://github.com/hyattpd/Prodigal")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/stamatak/standard-RAxML.git")
+ (url "https://github.com/stamatak/standard-RAxML")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/deweylab/RSEM.git")
+ (url "https://github.com/deweylab/RSEM")
(commit (string-append "v" version))))
(sha256
(base32 "1jlq11d1p8qp64w75yj8cnbbd1a93viq10pzsbwal7vdn8fg13j1"))
;; There are no release tarballs nor tags.
(method git-fetch)
(uri (git-reference
- (url "https://github.com/wanpinglee/MOSAIK.git")
+ (url "https://github.com/wanpinglee/MOSAIK")
(commit commit)))
(file-name (string-append name "-" version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ncbi/ngs.git")
+ (url "https://github.com/ncbi/ngs")
(commit version)))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ncbi/ncbi-vdb.git")
+ (url "https://github.com/ncbi/ncbi-vdb")
(commit version)))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/chrchang/plink-ng.git")
+ (url "https://github.com/chrchang/plink-ng")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/smithlabcode/smithlab_cpp.git")
+ (url "https://github.com/smithlabcode/smithlab_cpp")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ncbi/sra-tools.git")
+ (url "https://github.com/ncbi/sra-tools")
(commit version)))
(file-name (git-file-name name version))
(sha256
(define-public seqmagick
(package
(name "seqmagick")
- (version "0.7.0")
+ (version "0.8.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "seqmagick" version))
(sha256
(base32
- "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5"))))
+ "0pf98da7i59q47gwrbx0wjk6xlvbybiwphw80w7h4ydjj0579a2b"))))
(build-system python-build-system)
(inputs
`(("python-biopython" ,python-biopython)))
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/lh3/seqtk.git")
+ (url "https://github.com/lh3/seqtk")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/amplab/snap.git")
+ (url "https://github.com/amplab/snap")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/biocore/sortmerna.git")
+ (url "https://github.com/biocore/sortmerna")
(commit version)))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/alexdobin/STAR.git")
+ (url "https://github.com/alexdobin/STAR")
(commit version)))
(file-name (git-file-name name version))
(sha256
;; The Pypi version does not include tests.
(method git-fetch)
(uri (git-reference
- (url "https://github.com/fhcrc/taxtastic.git")
+ (url "https://github.com/fhcrc/taxtastic")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/hms-dbmi/scde.git")
+ (url "https://github.com/hms-dbmi/scde")
(commit version)))
(file-name (git-file-name name version))
(sha256
(define-public r-dexseq
(package
(name "r-dexseq")
- (version "1.34.0")
+ (version "1.34.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DEXSeq" version))
(sha256
(base32
- "1inyxb89hd5bn0sl7a9qbv9d1g40z4v1s9qwxkcsx5c79fl04n1h"))))
+ "1m03awaw06mfv5gszq23k5apsqqzjqa5rcwp20y4xbpl7bywpsyl"))))
(properties `((upstream-name . "DEXSeq")))
(build-system r-build-system)
(propagated-inputs
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/torognes/vsearch.git")
+ (url "https://github.com/torognes/vsearch")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(define-public r-biocviews
(package
(name "r-biocviews")
- (version "1.56.0")
+ (version "1.56.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biocViews" version))
(sha256
(base32
- "1h4cmfbff79v9xrh271dp3rv0877ris06lmkvc39kqzj7yjsh7c2"))))
+ "0kw0qfm1fw5yv2rbz6x23431rh0fnzj66f2bls7j285biyjmmx7w"))))
(properties
`((upstream-name . "biocViews")))
(build-system r-build-system)
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")
- (version "1.24.0")
+ (version "1.24.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomeInfoDb" version))
(sha256
(base32
- "0ab92nq7lvhvhgp512qhiiphpby0b17c666qska6p8a636zzmqiv"))))
+ "1cqs53p4m5q1dr59war72bccphy01ilw4xra24fmngrv4x32rznd"))))
(properties
`((upstream-name . "GenomeInfoDb")))
(build-system r-build-system)
(define-public r-limma
(package
(name "r-limma")
- (version "3.44.1")
+ (version "3.44.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "limma" version))
(sha256
(base32
- "0l6f6lz1rghj8c5s14ljbnmsrwz27fi6a7g42n15n3d3msvflw36"))))
+ "09fnqxx4rzq5n447aqg2l6y0idfwgz2jxz99sifxsr2q8afzbcj6"))))
(build-system r-build-system)
(home-page "http://bioinf.wehi.edu.au/limma")
(synopsis "Package for linear models for microarray and RNA-seq data")
(define-public r-annotationdbi
(package
(name "r-annotationdbi")
- (version "1.50.0")
+ (version "1.50.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationDbi" version))
(sha256
(base32
- "10gplxal0qphcn29azv0i6hiim9q45lmhzvhhhsnwfhwpgja7p05"))))
+ "0qcxfn4pvaksna0nvxr74ysn2wzaxn732pkhd6ffrj8pwhkhy5p3"))))
(properties
`((upstream-name . "AnnotationDbi")))
(build-system r-build-system)
(define-public r-biomart
(package
(name "r-biomart")
- (version "2.44.0")
+ (version "2.44.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biomaRt" version))
(sha256
(base32
- "0ag26q9283p9mfz4zx8qnx1w7b7ilmsb8wyx737z9cqy9a0i57wj"))))
+ "0np4nh3gj60mgb6312z7x0z9fg5bhrhw872sp3dzgmqc8q8b84iz"))))
(properties
`((upstream-name . "biomaRt")))
(build-system r-build-system)
(define-public r-delayedarray
(package
(name "r-delayedarray")
- (version "0.14.0")
+ (version "0.14.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DelayedArray" version))
(sha256
(base32
- "1lz7a0rrlfv3w44n073mk8pw39z7lfs0njdxp5vpp0rdsmvdf1qk"))))
+ "0xi0i621hrl7k9rsc8x8nc3ib74sk8hxhbyr2lxqclw45pk95s7v"))))
(properties
`((upstream-name . "DelayedArray")))
(build-system r-build-system)
(define-public r-summarizedexperiment
(package
(name "r-summarizedexperiment")
- (version "1.18.1")
+ (version "1.18.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "SummarizedExperiment" version))
(sha256
(base32
- "07rc79k5dp0dnf4dvsxif995aa9cgfkf13yf84qnwl64k9pf3c2c"))))
+ "1raw5ycigr6gjgzn3kx3jls5hzww10fhnwd8c17c20hmhirf13rw"))))
(properties
`((upstream-name . "SummarizedExperiment")))
(build-system r-build-system)
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
- (version "1.40.0")
+ (version "1.40.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
- "09ffsflk2yhhj9ivm028y3qdkvv8idgxpm4il3y9rym7shc8b3f8"))))
+ "0zm7q957g952qyfqmvf27sldsnq6sqd0wlgnqzvmxayg9pxh0l0z"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
("r-seqpattern" ,r-seqpattern)))
(native-inputs
`(("r-knitr" ,r-knitr)))
- (home-page "http://bioinformatics.mdc-berlin.de/genomation/")
+ (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
(synopsis "Summary, annotation and visualization of genomic data")
(description
"This package provides a package for summary and annotation of genomic
(arguments `(#:substitutable? #f))
(native-inputs
`(("r-knitr" ,r-knitr)))
- (home-page "http://bioinformatics.mdc-berlin.de/genomation/")
+ (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
(synopsis "Experimental data for use with the genomation package")
(description
"This package contains experimental genetic data for use with the
throughput genetic sequencing data sets using regression methods.")
(license license:artistic2.0)))
-(define-public r-qtl
- (package
- (name "r-qtl")
- (version "1.46-2")
- (source
- (origin
- (method url-fetch)
- (uri (string-append "mirror://cran/src/contrib/qtl_"
- version ".tar.gz"))
- (sha256
- (base32
- "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a"))))
- (build-system r-build-system)
- (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
-genes contributing to variation in quantitative traits (so-called
-quantitative trait loci, QTLs).
-
-Using a hidden Markov model, R/qtl estimates genetic maps, to
-identify genotyping errors, and to perform single-QTL and two-QTL,
-two-dimensional genome scans.")
- (license license:gpl3)))
-
-(define-public r-qtl2
- (package
- (name "r-qtl2")
- (version "0.20")
- (source (origin
- (method git-fetch)
- ;; Not yet available in cran.
- (uri (git-reference
- (url "https://github.com/rqtl/qtl2.git")
- (commit version)))
- (file-name (git-file-name name version))
- (sha256
- (base32 "0l1asr28q25jzbwrbg5490962sg3y4sjrd0qf09p78ws1aq8vfs0"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-data-table" ,r-data-table)
- ("r-jsonlite" ,r-jsonlite)
- ("r-rcpp" ,r-rcpp)
- ("r-rcppeigen" ,r-rcppeigen)
- ("r-rsqlite" ,r-rsqlite)
- ("r-yaml" ,r-yaml)))
- (home-page "https://kbroman.org/qtl2/")
- (synopsis
- "QTL analysis software for high-dimensional data and complex cross designs")
- (description
- "R/qtl2 (aka qtl2) is a reimplementation of the QTL analysis software
-R/qtl, to better handle high-dimensional data and complex cross designs.")
- (license license:gpl3)))
-
(define-public r-zlibbioc
(package
(name "r-zlibbioc")
("r-rtracklayer" ,r-rtracklayer)
("r-rmarkdown" ,r-rmarkdown)
("r-s4vectors" ,r-s4vectors)
- ("pandoc" ,ghc-pandoc)))
+ ("pandoc" ,pandoc)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(synopsis "RNA-centric annotation system")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ManuSetty/ChIPKernels.git")
+ (url "https://github.com/ManuSetty/ChIPKernels")
(commit commit)))
(file-name (string-append name "-" version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ManuSetty/SeqGL.git")
+ (url "https://github.com/ManuSetty/SeqGL")
(commit version)))
(file-name (git-file-name name version))
(sha256
(define-public r-rhdf5
(package
(name "r-rhdf5")
- (version "2.32.0")
+ (version "2.32.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rhdf5" version))
(sha256
(base32
- "097znwl95y2vd6asyqxs62m7binwxqmna7ss0302yl3b0s72skcy"))))
+ "1v6ygi0avh3gmaj2ld2nr7vww4ipw39b5kqci9w27i3ja985lb8j"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rhdf5lib" ,r-rhdf5lib)))
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/arq5x/bits.git")
+ (url "https://github.com/arq5x/bits")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/smithlabcode/piranha.git")
+ (url "https://github.com/smithlabcode/piranha")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/smithlabcode/smithlab_cpp.git")
+ (url "https://github.com/smithlabcode/smithlab_cpp")
(commit commit)))
(file-name (string-append "smithlab_cpp-" commit "-checkout"))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ekg/filevercmp.git")
+ (url "https://github.com/ekg/filevercmp")
(commit commit)))
(file-name (git-file-name name commit))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/vatlab/varianttools.git")
+ (url "https://github.com/vatlab/varianttools")
;; There is no tag corresponding to version 3.1.2
(commit "813ae4a90d25b69abc8a40f4f70441fe09015249")))
(file-name (git-file-name name version))
unmodeled, or latent sources of noise.")
(license license:artistic2.0)))
-(define-public r-seqminer
- (package
- (name "r-seqminer")
- (version "8.0")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "seqminer" version))
- (sha256
- (base32
- "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
- (build-system r-build-system)
- (inputs
- `(("zlib" ,zlib)))
- (home-page "http://seqminer.genomic.codes")
- (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
- (description
- "This package provides tools to integrate nucleotide sequencing
-data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
- ;; Any version of the GPL is acceptable
- (license (list license:gpl2+ license:gpl3+))))
-
(define-public r-raremetals2
(package
(name "r-raremetals2")
trait.")
(license license:gpl3)))
-(define-public r-maldiquant
- (package
- (name "r-maldiquant")
- (version "1.19.3")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "MALDIquant" version))
- (sha256
- (base32
- "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))
- (properties `((upstream-name . "MALDIquant")))
- (build-system r-build-system)
- (home-page "https://cran.r-project.org/web/packages/MALDIquant")
- (synopsis "Quantitative analysis of mass spectrometry data")
- (description
- "This package provides a complete analysis pipeline for matrix-assisted
-laser desorption/ionization-time-of-flight (MALDI-TOF) and other
-two-dimensional mass spectrometry data. In addition to commonly used plotting
-and processing methods it includes distinctive features, namely baseline
-subtraction methods such as morphological filters (TopHat) or the
-statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
-alignment using warping functions, handling of replicated measurements as well
-as allowing spectra with different resolutions.")
- (license license:gpl3+)))
-
(define-public r-protgenerics
(package
(name "r-protgenerics")
(define-public r-mzr
(package
(name "r-mzr")
- (version "2.20.0")
+ (version "2.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mzR" version))
(sha256
(base32
- "1cwd7phlc5jbx6r6cznyfbdpvcin5fvsaasbbi65zn0s92a80r13"))
+ "1r8j8yiz5lcan7j4h37sza2kwczl48dxvld3da3ghjjq67cdc2cm"))
(modules '((guix build utils)))
(snippet
'(begin
#t)))))
(inputs
`(;; Our default boost package won't work here, unfortunately, even with
- ;; mzR version 2.20.0.
+ ;; mzR version 2.22.0.
("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources
("zlib" ,zlib)))
(propagated-inputs
("r-rcpp" ,r-rcpp)
("r-rhdf5lib" ,r-rhdf5lib)
("r-zlibbioc" ,r-zlibbioc)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/sneumann/mzR/")
(synopsis "Parser for mass spectrometry data files")
(description
and irregular enzymatic cleavages, mass measurement accuracy, etc.")
(license license:artistic2.0)))
-(define-public r-seurat
- (package
- (name "r-seurat")
- (version "3.1.5")
- (source (origin
- (method url-fetch)
- (uri (cran-uri "Seurat" version))
- (sha256
- (base32
- "1lbq2pqhb6ih6iqawlnzdh05zff71pwbw1cpfv2sld3pd7kz0zkm"))))
- (properties `((upstream-name . "Seurat")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-ape" ,r-ape)
- ("r-cluster" ,r-cluster)
- ("r-cowplot" ,r-cowplot)
- ("r-fitdistrplus" ,r-fitdistrplus)
- ("r-future" ,r-future)
- ("r-future-apply" ,r-future-apply)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggrepel" ,r-ggrepel)
- ("r-ggridges" ,r-ggridges)
- ("r-httr" ,r-httr)
- ("r-ica" ,r-ica)
- ("r-igraph" ,r-igraph)
- ("r-irlba" ,r-irlba)
- ("r-kernsmooth" ,r-kernsmooth)
- ("r-leiden" ,r-leiden)
- ("r-lmtest" ,r-lmtest)
- ("r-mass" ,r-mass)
- ("r-matrix" ,r-matrix)
- ("r-patchwork" ,r-patchwork)
- ("r-pbapply" ,r-pbapply)
- ("r-plotly" ,r-plotly)
- ("r-png" ,r-png)
- ("r-rann" ,r-rann)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rcpp" ,r-rcpp)
- ("r-rcppannoy" ,r-rcppannoy)
- ("r-rcppeigen" ,r-rcppeigen)
- ("r-rcppprogress" ,r-rcppprogress)
- ("r-reticulate" ,r-reticulate)
- ("r-rlang" ,r-rlang)
- ("r-rocr" ,r-rocr)
- ("r-rsvd" ,r-rsvd)
- ("r-rtsne" ,r-rtsne)
- ("r-scales" ,r-scales)
- ("r-sctransform" ,r-sctransform)
- ("r-tsne" ,r-tsne)
- ("r-uwot" ,r-uwot)))
- (home-page "http://www.satijalab.org/seurat")
- (synopsis "Seurat is an R toolkit for single cell genomics")
- (description
- "This package is an R package designed for QC, analysis, and
-exploration of single cell RNA-seq data. It easily enables widely-used
-analytical techniques, including the identification of highly variable genes,
-dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
-algorithms; density clustering, hierarchical clustering, k-means, and the
-discovery of differentially expressed genes and markers.")
- (license license:gpl3)))
-
(define-public r-aroma-light
(package
(name "r-aroma-light")
(define-public r-annotationhub
(package
(name "r-annotationhub")
- (version "2.20.0")
+ (version "2.20.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationHub" version))
(sha256
(base32
- "0r4xzf93bm9cpys5cg70wg0b8hxli80hvqwgh4hzbd45yyf5c4wz"))))
+ "04bz91m2wx1zm61rvpr0syyklz232fw74wrl73d965wi3x8fyda5"))))
(properties `((upstream-name . "AnnotationHub")))
(build-system r-build-system)
(propagated-inputs
(define-public r-gage
(package
(name "r-gage")
- (version "2.37.0")
+ (version "2.38.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gage" version))
(sha256
(base32
- "1zfaas4x6g7wiml6cmxa7b4f43az9s0lrw80k6sf7c96hsh1jijr"))))
+ "1bqmvjiya1df0b3h491lp1jxahiyidvaf9n094z0sk84x5y3xh2p"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
+ ("r-go-db" ,r-go-db)
("r-graph" ,r-graph)
("r-keggrest" ,r-keggrest)))
(home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
(define-public r-complexheatmap
(package
(name "r-complexheatmap")
- (version "2.4.2")
+ (version "2.4.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ComplexHeatmap" version))
(sha256
(base32
- "01jxxwxhf9n8baxgja4rb592p5210s4ppd7a5b4xby5aalhzkr0l"))))
+ "1gx0hzrkla92pgmfkrm2zp0ccnhizq6rs26zgzpi5x8a5lvghh5q"))))
(properties
`((upstream-name . "ComplexHeatmap")))
(build-system r-build-system)
(define-public r-gviz
(package
(name "r-gviz")
- (version "1.30.3")
+ (version "1.32.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Gviz" version))
(sha256
(base32
- "0c9i26h5czm60n1bxzmdxxpywcj0sig6wcj913pb41mr83bbgra3"))))
+ "0cgkp0ciyy2qykqgh3vzp5mx9b4vsvacjh2jnsj3wldiapzlz08a"))))
(properties `((upstream-name . "Gviz")))
(build-system r-build-system)
(propagated-inputs
("r-biovizbase" ,r-biovizbase)
("r-bsgenome" ,r-bsgenome)
("r-digest" ,r-digest)
+ ("r-ensembldb" ,r-ensembldb)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicalignments" ,r-genomicalignments)
("r-genomicfeatures" ,r-genomicfeatures)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)
("r-xvector" ,r-xvector)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/Gviz")
(synopsis "Plotting data and annotation information along genomic coordinates")
(description
(define-public r-gwascat
(package
(name "r-gwascat")
- (version "2.18.0")
+ (version "2.20.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gwascat" version))
(sha256
(base32
- "038vhfsk2vs7inn5di093cmjbb81k7j0af385sg7l01jj70bdqq1"))))
+ "1cq5cmdrf0a0arr841yvkh6d8drc15p7mif1afr215l1s3y2dwd4"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicfeatures" ,r-genomicfeatures)
("r-genomicranges" ,r-genomicranges)
- ("r-homo-sapiens" ,r-homo-sapiens)
+ ("r-ggplot2" ,r-ggplot2)
("r-iranges" ,r-iranges)
("r-rsamtools" ,r-rsamtools)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/gwascat")
(synopsis "Tools for data in the EMBL-EBI GWAS catalog")
(description
(define-public r-sushi
(package
(name "r-sushi")
- (version "1.24.0")
+ (version "1.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Sushi" version))
(sha256
(base32
- "15xng21hd09fb234ravrry3b872zg82w8x9lijxab9n96xihcpz5"))))
+ "17j3d5qjq5nbv99by5mq8rwr0jgh2jyyfn2nwxmwgzlmk3lgi1rb"))))
(properties `((upstream-name . "Sushi")))
(build-system r-build-system)
(propagated-inputs
(define-public r-fithic
(package
(name "r-fithic")
- (version "1.12.0")
+ (version "1.14.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "FitHiC" version))
(sha256
(base32
- "1irwkwi4afdj395134k31mvx7c2vpdd0rv8zrblnldascdsb04kc"))))
+ "1dffkdxm08wq4kjd9j2v2625x3p6vbrk33a2zx94pwpgkghr72yp"))))
(properties `((upstream-name . "FitHiC")))
(build-system r-build-system)
(propagated-inputs
`(("r-data-table" ,r-data-table)
("r-fdrtool" ,r-fdrtool)
("r-rcpp" ,r-rcpp)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/FitHiC")
(synopsis "Confidence estimation for intra-chromosomal contact maps")
(description
(define-public r-hitc
(package
(name "r-hitc")
- (version "1.30.0")
+ (version "1.32.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "HiTC" version))
(sha256
(base32
- "0byahi0fz0dzjyklz8v9whax9ygg7gwb4pl1j3zbl6z8a9qx8pps"))))
+ "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy"))))
(properties `((upstream-name . "HiTC")))
(build-system r-build-system)
(propagated-inputs
(define-public r-hdf5array
(package
(name "r-hdf5array")
- (version "1.14.4")
+ (version "1.16.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "HDF5Array" version))
(sha256
(base32
- "0ib0grhd9zbrn0dkrm4aa7qj7h0y6z1dvyx1ab3w6vczw7xghsfb"))))
+ "01767v90nl0499jcicpxngbbs0af5p9c5aasi5va01w3v5bnqddn"))))
(properties `((upstream-name . "HDF5Array")))
(build-system r-build-system)
(inputs
(define-public r-rhdf5lib
(package
(name "r-rhdf5lib")
- (version "1.8.0")
+ (version "1.10.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rhdf5lib" version))
(sha256
(base32
- "17lhwnm9rqsvbqkvwp0m07vjrk63a4389p2y39zffv8fgznxqzd7"))
+ "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9"))
(modules '((guix build utils)))
(snippet
'(begin
;; Delete bundled binaries
- (delete-file-recursively "src/winlib/")
+ (delete-file-recursively "src/wininclude/")
+ (delete-file-recursively "src/winlib-4.9.3/")
+ (delete-file-recursively "src/winlib-8.3.0/")
+ (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
#t))))
(properties `((upstream-name . "Rhdf5lib")))
(build-system r-build-system)
(for-each delete-file '("configure" "configure.ac"))
;; Do not make other packages link with the proprietary libsz.
(substitute* "R/zzz.R"
- (("'\"%s/libhdf5.a\" \"%s/libsz.a\" -lz'")
- "'\"%s/libhdf5.a\" \"%s/libhdf5.a\" -lz'")
- (("'\"%s/libhdf5_cpp.a\" \"%s/libhdf5.a\" \"%s/libsz.a\" -lz'")
- "'\"%s/libhdf5_cpp.a\" \"%s/libhdf5.a\" \"%s/libhdf5.a\" -lz'")
- (("'%s/libhdf5_hl.a %s/libhdf5.a %s/libsz.a -lz'")
- "'%s/libhdf5_hl.a %s/libhdf5.a %s/libhdf5.a -lz'")
- (("'%s/libhdf5_hl_cpp.a %s/libhdf5_hl.a %s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a -lz'")
- "'%s/libhdf5_hl_cpp.a %s/libhdf5_hl.a %s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a -lz'"))
+ ((" \"%s/libsz.a\"") ""))
(with-directory-excursion "src"
(invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
(rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
"C Compiler: GCC\n"))
(rename-file "Makevars.in" "Makevars")
(substitute* "Makevars"
+ (("@ZLIB_LIB@") "-lz")
+ (("@ZLIB_INCLUDE@") "")
(("HDF5_CXX_LIB=.*")
(string-append "HDF5_CXX_LIB="
(assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
(propagated-inputs
`(("hdf5" ,hdf5-1.10)))
(native-inputs
- `(("hdf5-source" ,(package-source hdf5-1.10))))
+ `(("hdf5-source" ,(package-source hdf5-1.10))
+ ("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/Rhdf5lib")
(synopsis "HDF5 library as an R package")
(description "This package provides C and C++ HDF5 libraries for use in R
(define-public r-beachmat
(package
(name "r-beachmat")
- (version "2.2.1")
+ (version "2.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "beachmat" version))
(sha256
(base32
- "1bpnlw2kdy9yc2vq948k980r0j25ipb80llhvn0j3kxjiwyfgs3i"))))
+ "1vl6jbf9ia78cm4ikdb8vz04jv4b46zhvg5i006c63a9pzw7zhxi"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-delayedarray" ,r-delayedarray)
("r-matrix" ,r-matrix)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/beachmat")
(synopsis "Compiling Bioconductor to handle each matrix type")
(description "This package provides a consistent C++ class interface for a
(define-public r-singlecellexperiment
(package
(name "r-singlecellexperiment")
- (version "1.8.0")
+ (version "1.10.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "SingleCellExperiment" version))
(sha256
(base32
- "11pqb3cigi9xbhxq2k3n7z23v1ibd03ws1lcrh5c5ffgb33nlyw5"))))
+ "092wvk11n7pa234vlwhxm3gdi4k3sbnz1splhxalbdhz3jf02zfp"))))
(properties
`((upstream-name . "SingleCellExperiment")))
(build-system r-build-system)
`(("r-biocgenerics" ,r-biocgenerics)
("r-s4vectors" ,r-s4vectors)
("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/SingleCellExperiment")
(synopsis "S4 classes for single cell data")
(description "This package defines an S4 class for storing data from
(define-public r-scater
(package
(name "r-scater")
- (version "1.14.6")
+ (version "1.16.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "scater" version))
(sha256
(base32
- "0sxd1s8wdlj9926bagq4crjrk1nnmh3j3bhgrw160zfgc3y8pzck"))))
+ "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33"))))
(build-system r-build-system)
(propagated-inputs
`(("r-beachmat" ,r-beachmat)
("r-ggplot2" ,r-ggplot2)
("r-matrix" ,r-matrix)
("r-rcpp" ,r-rcpp)
+ ("r-rlang" ,r-rlang)
("r-s4vectors" ,r-s4vectors)
("r-singlecellexperiment" ,r-singlecellexperiment)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-viridis" ,r-viridis)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/davismcc/scater")
(synopsis "Single-cell analysis toolkit for gene expression data in R")
(description "This package provides a collection of tools for doing
(define-public r-scran
(package
(name "r-scran")
- (version "1.14.6")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scran" version))
(sha256
(base32
- "1y8wlgk5zbv7c7gcp0ahfpbh9lifab7y3zwf0093fzaw7vr1y6cr"))))
+ "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-beachmat" ,r-beachmat)
("r-dqrng" ,r-dqrng)
("r-edger" ,r-edger)
("r-igraph" ,r-igraph)
+ ("r-iranges" ,r-iranges)
("r-limma" ,r-limma)
("r-matrix" ,r-matrix)
("r-rcpp" ,r-rcpp)
("r-singlecellexperiment" ,r-singlecellexperiment)
("r-statmod" ,r-statmod)
("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/scran")
(synopsis "Methods for single-cell RNA-Seq data analysis")
(description "This package implements a variety of low-level analyses of
(define-public r-delayedmatrixstats
(package
(name "r-delayedmatrixstats")
- (version "1.8.0")
+ (version "1.10.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DelayedMatrixStats" version))
(sha256
(base32
- "0mv2rl6a6l404piabcazxz1s6ars016pxhjf5v40hhr6y1r0wbqy"))))
+ "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx"))))
(properties
`((upstream-name . "DelayedMatrixStats")))
(build-system r-build-system)
("r-matrix" ,r-matrix)
("r-matrixstats" ,r-matrixstats)
("r-s4vectors" ,r-s4vectors)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
(synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
(description
memory usage and processing time is minimized.")
(license license:expat)))
-(define-public r-phangorn
- (package
- (name "r-phangorn")
- (version "2.5.5")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "phangorn" version))
- (sha256
- (base32
- "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-ape" ,r-ape)
- ("r-fastmatch" ,r-fastmatch)
- ("r-igraph" ,r-igraph)
- ("r-magrittr" ,r-magrittr)
- ("r-matrix" ,r-matrix)
- ("r-quadprog" ,r-quadprog)
- ("r-rcpp" ,r-rcpp)))
- (home-page "https://github.com/KlausVigo/phangorn")
- (synopsis "Phylogenetic analysis in R")
- (description
- "Phangorn is a package for phylogenetic analysis in R. It supports
-estimation of phylogenetic trees and networks using Maximum Likelihood,
-Maximum Parsimony, distance methods and Hadamard conjugation.")
- (license license:gpl2+)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/rajewsky-lab/dropbead.git")
+ (url "https://github.com/rajewsky-lab/dropbead")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/lomereiter/htslib.git")
+ (url "https://github.com/lomereiter/htslib")
(commit commit)))
(file-name (string-append "htslib-" version "-checkout"))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/lomereiter/sambamba.git")
+ (url "https://github.com/lomereiter/sambamba")
(commit (string-append "v" version))))
(file-name (string-append name "-" version "-checkout"))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/biod/BioD.git")
+ (url "https://github.com/biod/BioD")
(commit commit)))
(file-name (string-append "biod-"
(string-take commit 9)
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/KlugerLab/Ritornello.git")
+ (url "https://github.com/KlugerLab/Ritornello")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/FelixKrueger/TrimGalore.git")
+ (url "https://github.com/FelixKrueger/TrimGalore")
(commit version)))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/3DGenomes/TADbit.git")
+ (url "https://github.com/3DGenomes/TADbit")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ENCODE-DCC/kentUtils.git")
+ (url "https://github.com/ENCODE-DCC/kentUtils")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/aboyle/F-seq.git")
+ (url "https://github.com/aboyle/F-seq")
(commit commit)))
(file-name (string-append name "-" version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/FelixKrueger/Bismark.git")
+ (url "https://github.com/FelixKrueger/Bismark")
(commit version)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(snippet
'(begin
(for-each delete-file (find-files "." "\\.exe$"))
+ ;; Some files in the original tarball have restrictive
+ ;; permissions, which makes repackaging fail
+ (for-each (lambda (file) (chmod file #o644)) (find-files "."))
#t))))
(build-system gnu-build-system)
(arguments
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/pachterlab/kallisto.git")
+ (url "https://github.com/pachterlab/kallisto")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/Kingsford-Group/libgff.git")
+ (url "https://github.com/Kingsford-Group/libgff")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/kingsfordgroup/sailfish.git")
+ (url "https://github.com/kingsfordgroup/sailfish")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
("rapmap" ,(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/COMBINE-lab/RapMap.git")
+ (url "https://github.com/COMBINE-lab/RapMap")
(commit (string-append "sf-v" version))))
(file-name (string-append "rapmap-sf-v" version "-checkout"))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/COMBINE-lab/staden-io_lib.git")
+ (url "https://github.com/COMBINE-lab/staden-io_lib")
(commit (string-append "v" version))))
(file-name (string-append name "-" version "-checkout"))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/COMBINE-lab/salmon.git")
+ (url "https://github.com/COMBINE-lab/salmon")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
("rapmap" ,(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/COMBINE-lab/RapMap.git")
+ (url "https://github.com/COMBINE-lab/RapMap")
(commit (string-append "salmon-v" version))))
(file-name (string-append "rapmap-salmon-v" version "-checkout"))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/linnarsson-lab/loompy.git")
+ (url "https://github.com/linnarsson-lab/loompy")
(commit version)))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/cmzmasek/forester.git")
+ (url "https://github.com/cmzmasek/forester")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(native-inputs
`(("java-junit" ,java-junit)
("java-hamcrest-core" ,java-hamcrest-core)))
- (home-page "http://biojava.org")
+ (home-page "https://biojava.org")
(synopsis "Core libraries of Java framework for processing biological data")
(description "BioJava is a project dedicated to providing a Java framework
for processing biological data. It provides analytical and statistical
(native-inputs
`(("java-junit" ,java-junit)
("java-hamcrest-core" ,java-hamcrest-core)))
- (home-page "http://biojava.org")
+ (home-page "https://biojava.org")
(synopsis "Biojava interface to the forester phylogenomics library")
(description "The phylo module provides a biojava interface layer to the
forester phylogenomics library for constructing phylogenetic trees.")))
(native-inputs
`(("java-junit" ,java-junit)
("java-hamcrest-core" ,java-hamcrest-core)))
- (home-page "http://biojava.org")
+ (home-page "https://biojava.org")
(synopsis "Biojava API for genetic sequence alignment")
(description "The alignment module of BioJava provides an API that
contains
(native-inputs
`(("java-junit" ,java-junit)
("java-hamcrest-core" ,java-hamcrest-core)))
- (home-page "http://biojava.org")
+ (home-page "https://biojava.org")
(synopsis "Biojava interface to the forester phylogenomics library")
(description "The phylo module provides a biojava interface layer to the
forester phylogenomics library for constructing phylogenetic trees.")))
(native-inputs
`(("java-junit" ,java-junit)
("java-hamcrest-core" ,java-hamcrest-core)))
- (home-page "http://biojava.org")
+ (home-page "https://biojava.org")
(synopsis "Biojava API for genetic sequence alignment")
(description "The alignment module of BioJava provides an API that
contains
("r-rtracklayer" ,r-rtracklayer)
("r-rjson" ,r-rjson)
("salmon" ,salmon)
- ("ghc-pandoc" ,ghc-pandoc)
- ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
+ ("pandoc" ,pandoc)
+ ("pandoc-citeproc" ,pandoc-citeproc)
("python-wrapper" ,python-wrapper)
("python-pyyaml" ,python-pyyaml)))
- (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
+ (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
(synopsis "Analysis pipeline for RNA sequencing experiments")
(description "PiGX RNAseq is an analysis pipeline for preprocessing and
reporting for RNA sequencing experiments. It is easy to use and produces high
(define-public pigx-chipseq
(package
(name "pigx-chipseq")
- (version "0.0.42")
+ (version "0.0.43")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
"/pigx_chipseq-" version ".tar.gz"))
(sha256
(base32
- "0xbvgqpk32a8iczhvac56cacr46rdkqb0allhhpvmj940idf72bi"))))
+ "0426i31b7mqqkbss5dgrvf5prkj4z1qrd7yrpd27vybs01xhdlks"))))
(build-system gnu-build-system)
;; parts of the tests rely on access to the network
(arguments '(#:tests? #f))
("macs" ,macs)
("multiqc" ,multiqc)
("perl" ,perl)
- ("ghc-pandoc" ,ghc-pandoc)
- ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
+ ("pandoc" ,pandoc)
+ ("pandoc-citeproc" ,pandoc-citeproc)
("fastqc" ,fastqc)
("bowtie" ,bowtie)
("idr" ,idr)
("kentutils" ,kentutils)))
(native-inputs
`(("python-pytest" ,python-pytest)))
- (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
+ (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
(synopsis "Analysis pipeline for ChIP sequencing experiments")
(description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak
calling and reporting for ChIP sequencing experiments. It is easy to use and
(define-public pigx-bsseq
(package
(name "pigx-bsseq")
- (version "0.0.10")
+ (version "0.1.2")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/"
"/pigx_bsseq-" version ".tar.gz"))
(sha256
(base32
- "0l97wvkq4diq8lcarraj33bby1zzf0w804jwi8mlc5qddp8idwhy"))))
+ "0mpzlay2d5cjpmrcp7knff6rg1c2mqszd638n7lw0mc0cycbp9f8"))))
(build-system gnu-build-system)
(arguments
- `(#:phases
+ `(;; TODO: tests currently require 12+GB of RAM. See
+ ;; https://github.com/BIMSBbioinfo/pigx_bsseq/issues/164
+ #:tests? #f
+ #:phases
(modify-phases %standard-phases
(add-before 'check 'set-timezone
;; The readr package is picky about timezones.
("r-annotationhub" ,r-annotationhub)
("r-dt" ,r-dt)
("r-genomation" ,r-genomation)
+ ("r-ggrepel" ,r-ggrepel)
("r-methylkit" ,r-methylkit)
("r-rtracklayer" ,r-rtracklayer)
("r-rmarkdown" ,r-rmarkdown)
("r-bookdown" ,r-bookdown)
("r-ggplot2" ,r-ggplot2)
("r-ggbio" ,r-ggbio)
- ("ghc-pandoc" ,ghc-pandoc)
- ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
+ ("pandoc" ,pandoc)
+ ("pandoc-citeproc" ,pandoc-citeproc)
("python-wrapper" ,python-wrapper)
("python-pyyaml" ,python-pyyaml)
("snakemake" ,snakemake)
("bismark" ,bismark)
- ("fastqc" ,fastqc)
("bowtie" ,bowtie)
+ ("bwa-meth" ,bwa-meth)
+ ("fastqc" ,fastqc)
+ ("methyldackel" ,methyldackel)
+ ("multiqc" ,multiqc)
("trim-galore" ,trim-galore)
("cutadapt" ,cutadapt)
+ ("samblaster" ,samblaster)
("samtools" ,samtools)))
- (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
+ (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
(synopsis "Bisulfite sequencing pipeline from fastq to methylation reports")
(description "PiGx BSseq is a data processing pipeline for raw fastq read
data of bisulfite experiments; it produces reports on aggregate methylation
("python-magic" ,python-magic)
("python-numpy" ,python-numpy)
("python-loompy" ,python-loompy)
- ("ghc-pandoc" ,ghc-pandoc)
- ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
+ ("pandoc" ,pandoc)
+ ("pandoc-citeproc" ,pandoc-citeproc)
("samtools" ,samtools)
("snakemake" ,snakemake)
("star" ,star)
("r-singlecellexperiment" ,r-singlecellexperiment)
("r-stringr" ,r-stringr)
("r-yaml" ,r-yaml)))
- (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
+ (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
(synopsis "Analysis pipeline for single-cell RNA sequencing experiments")
(description "PiGX scRNAseq is an analysis pipeline for preprocessing and
quality control for single cell RNA sequencing experiments. The inputs are
("pigx-chipseq" ,pigx-chipseq)
("pigx-rnaseq" ,pigx-rnaseq)
("pigx-scrnaseq" ,pigx-scrnaseq)))
- (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
+ (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
(synopsis "Analysis pipelines for genomics")
(description "PiGx is a collection of genomics pipelines. It includes the
following pipelines:
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/jsh58/Genrich.git")
+ (url "https://github.com/jsh58/Genrich")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/splatlab/mantis.git")
+ (url "https://github.com/splatlab/mantis")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(supported-systems '("x86_64-linux"))
(license license:bsd-3))))
-(define-public r-diversitree
- (package
- (name "r-diversitree")
- (version "0.9-13")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "diversitree" version))
- (sha256
- (base32
- "00vi4klywi35hd170ksjv3xja3hqqbkcidcnrrlpgv4179k0azix"))))
- (build-system r-build-system)
- (native-inputs
- `(("gfortran" ,gfortran)))
- (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
- (propagated-inputs
- `(("r-ape" ,r-ape)
- ("r-desolve" ,r-desolve)
- ("r-rcpp" ,r-rcpp)
- ("r-subplex" ,r-subplex)))
- (home-page "https://www.zoology.ubc.ca/prog/diversitree")
- (synopsis "Comparative 'phylogenetic' analyses of diversification")
- (description "This package contains a number of comparative \"phylogenetic\"
-methods, mostly focusing on analysing diversification and character evolution.
-Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
-and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
-Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
-include Markov models of discrete and continuous trait evolution and constant
-rate speciation and extinction.")
- (license license:gpl2+)))
-
(define-public sjcount
;; There is no tag for version 3.2, nor is there a release archive.
(let ((commit "292d3917cadb3f6834c81e509c30e61cd7ead6e5")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/pervouchine/sjcount-full.git")
+ (url "https://github.com/pervouchine/sjcount-full")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(name "miniasm")
(version "0.3")
(source (origin
- (method url-fetch)
- (uri (string-append
- "https://github.com/lh3/miniasm/archive/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/lh3/miniasm")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
- (base32
- "0g89pa98dvh34idv7w1zv12bsbyr3a11c4qb1cdcz68gyda88s4v"))))
+ (base32
+ "04dv5wv8bhsw1imxwyd438bnn9kby7svp44nbcz8lsadzjjci5gs"))))
(build-system gnu-build-system)
(inputs
`(("zlib" ,zlib)))
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(install-file "miniasm" bin)
- (install-file "minidot" bin)))))))
+ (install-file "minidot" bin)
+ #t))))))
(home-page "https://github.com/lh3/miniasm")
(synopsis "Ultrafast de novo assembly for long noisy reads")
(description "Miniasm is a very fast OLC-based de novo assembler for noisy
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/BIMSBbioinfo/ciRcus.git")
+ (url "https://github.com/BIMSBbioinfo/ciRcus")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/gpertea/gffread.git")
+ (url "https://github.com/gpertea/gffread")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/gpertea/gclib.git")
+ (url "https://github.com/gpertea/gclib")
(commit commit)))
(file-name (git-file-name "gclib" version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/marvin-jens/find_circ.git")
+ (url "https://github.com/marvin-jens/find_circ")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/4dn-dcic/pairix.git")
+ (url "https://github.com/4dn-dcic/pairix")
(commit version)))
(file-name (git-file-name name version))
(sha256
;; Version 12 is not available on pypi.
(method git-fetch)
(uri (git-reference
- (url "https://github.com/deeptools/HiCMatrix.git")
+ (url "https://github.com/deeptools/HiCMatrix")
(commit version)))
(file-name (git-file-name name version))
(sha256
;; The latest version is not available on Pypi.
(method git-fetch)
(uri (git-reference
- (url "https://github.com/deeptools/HiCExplorer.git")
+ (url "https://github.com/deeptools/HiCExplorer")
(commit version)))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/renozao/xbioc.git")
+ (url "https://github.com/renozao/xbioc")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/shenorrLab/csSAM.git")
+ (url "https://github.com/shenorrLab/csSAM")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/shenorrLab/bseqsc.git")
+ (url "https://github.com/shenorrLab/bseqsc")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/rrwick/Porechop.git")
+ (url "https://github.com/rrwick/Porechop")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/arq5x/poretools.git")
+ (url "https://github.com/arq5x/poretools")
(commit commit)))
(file-name (git-file-name name version))
(sha256
of the Hierarchical Data Format (HDF5) standard.")
(license license:expat))))
-(define-public r-absfiltergsea
- (package
- (name "r-absfiltergsea")
- (version "1.5.1")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "AbsFilterGSEA" version))
- (sha256
- (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
- (properties `((upstream-name . "AbsFilterGSEA")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-deseq" ,r-deseq)
- ("r-limma" ,r-limma)
- ("r-rcpp" ,r-rcpp)
- ("r-rcpparmadillo" ,r-rcpparmadillo)))
- (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
- (synopsis "Improved false positive control of gene-permuting with absolute filtering")
- (description
- "This package provides a function that performs gene-permuting of a gene-set
-enrichment analysis (GSEA) calculation with or without the absolute filtering.
- Without filtering, users can perform (original) two-tailed or one-tailed
-absolute GSEA.")
- (license license:gpl2)))
-
(define-public jamm
(package
(name "jamm")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/mahmoudibrahim/JAMM.git")
+ (url "https://github.com/mahmoudibrahim/JAMM")
(commit (string-append "JAMMv" version))))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/rrwick/Filtlong.git")
+ (url "https://github.com/rrwick/Filtlong")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/jts/nanopolish.git")
+ (url "https://github.com/jts/nanopolish")
(commit commit)
(recursive? #t)))
(file-name (git-file-name name version))
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/etal/cnvkit.git")
+ (url "https://github.com/etal/cnvkit")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/KlugerLab/pyFIt-SNE.git")
+ (url "https://github.com/KlugerLab/pyFIt-SNE")
(commit version)))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/MikkelSchubert/adapterremoval.git")
+ (url "https://github.com/MikkelSchubert/adapterremoval")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/matsen/pplacer.git")
+ (url "https://github.com/matsen/pplacer")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ParkerLab/ataqv.git")
+ (url "https://github.com/ParkerLab/ataqv")
(commit version)))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/kcha/psiplot.git")
+ (url "https://github.com/kcha/psiplot")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/nanoporetech/ont_fast5_api.git")
+ (url "https://github.com/nanoporetech/ont_fast5_api")
(commit (string-append "release_" version))))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/phoenixding/tbsp.git")
+ (url "https://github.com/phoenixding/tbsp")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(string-append "HTS_LIB=" htslib-ref "/lib/libhts.a")
(string-append "INCLUDES= -I" htslib-ref "/include/htslib")
"HTS_HEADERS=" ; No need to check for headers here.
- (string-append "LIBPATH=-L. -L" htslib-ref "/include")))))
+ (string-append "LIBPATH=-L. -L" htslib-ref "/include"))
+ (invoke "g++" "-shared" "-o" "libtabixpp.so" "tabix.o" "-lhts")
+ (invoke "ar" "rcs" "libtabixpp.a" "tabix.o"))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
- (install-file "tabix++" bin))
- #t)))))
+ (let* ((out (assoc-ref outputs "out"))
+ (lib (string-append out "/lib"))
+ (bin (string-append out "/bin")))
+ (install-file "tabix++" bin)
+ (install-file "libtabixpp.so" lib)
+ (install-file "libtabixpp.a" lib)
+ (install-file "tabix.hpp" (string-append out "/include"))
+ (mkdir-p (string-append lib "/pkgconfig"))
+ (with-output-to-file (string-append lib "/pkgconfig/tabixpp.pc")
+ (lambda _
+ (format #t "prefix=~a~@
+ exec_prefix=${prefix}~@
+ libdir=${exec_prefix}/lib~@
+ includedir=${prefix}/include~@
+ ~@
+ ~@
+ Name: libtabixpp~@
+ Version: ~a~@
+ Description: C++ wrapper around tabix project~@
+ Libs: -L${libdir} -ltabixpp~@
+ Cflags: -I${includedir}~%"
+ out ,version)))
+ #t))))))
(home-page "https://github.com/ekg/tabixpp")
(synopsis "C++ wrapper around tabix project")
(description "This is a C++ wrapper around the Tabix project which abstracts
#:phases
(modify-phases %standard-phases
(delete 'configure) ; There is no configure phase.
+ (add-after 'unpack 'patch-source
+ (lambda _
+ (substitute* "Makefile"
+ (("-c ") "-c -fPIC "))
+ #t))
+ (add-after 'build 'build-dynamic
+ (lambda _
+ (invoke "g++"
+ "-shared" "-o" "libsmithwaterman.so"
+ "smithwaterman.o" "SmithWatermanGotoh.o"
+ "disorder.o" "BandedSmithWaterman.o"
+ "LeftAlign.o" "Repeats.o" "IndelAllele.o")))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(lib (string-append out "/lib")))
(install-file "smithwaterman" bin)
- (install-file "libsw.a" lib))
+ (for-each
+ (lambda (file)
+ (install-file file (string-append out "/include/smithwaterman")))
+ (find-files "." "\\.h$"))
+ (install-file "libsmithwaterman.so" lib)
+ (install-file "libsw.a" lib)
+ (mkdir-p (string-append lib "/pkgconfig"))
+ (with-output-to-file (string-append lib "/pkgconfig/smithwaterman.pc")
+ (lambda _
+ (format #t "prefix=~a~@
+ exec_prefix=${prefix}~@
+ libdir=${exec_prefix}/lib~@
+ includedir=${prefix}/include/smithwaterman~@
+ ~@
+ ~@
+ Name: smithwaterman~@
+ Version: ~a~@
+ Description: smith-waterman-gotoh alignment algorithm~@
+ Libs: -L${libdir} -lsmithwaterman~@
+ Cflags: -I${includedir}~%"
+ out ,version))))
#t)))))
(home-page "https://github.com/ekg/smithwaterman")
(synopsis "Implementation of the Smith-Waterman algorithm")
#:phases
(modify-phases %standard-phases
(delete 'configure) ; There is no configure phase.
+ (add-after 'unpack 'patch-source
+ (lambda _
+ (substitute* "Makefile"
+ (("-c ") "-c -fPIC "))
+ #t))
+ (add-after 'build 'build-dynamic
+ (lambda _
+ (invoke "g++"
+ "-shared" "-o" "libfastahack.so"
+ "Fasta.o" "FastaHack.o" "split.o" "disorder.o")))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
- (install-file "fastahack" bin))
+ (let* ((out (assoc-ref outputs "out"))
+ (lib (string-append out "/lib"))
+ (bin (string-append out "/bin")))
+ (mkdir-p (string-append out "/include/fastahack"))
+ (for-each
+ (lambda (file)
+ (install-file file (string-append out "/include/fastahack")))
+ (find-files "." "\\.h$"))
+ (install-file "fastahack" bin)
+ (install-file "libfastahack.so" lib)
+ (mkdir-p (string-append lib "/pkgconfig"))
+ (with-output-to-file (string-append lib "/pkgconfig/fastahack.pc")
+ (lambda _
+ (format #t "prefix=~a~@
+ exec_prefix=${prefix}~@
+ libdir=${exec_prefix}/lib~@
+ includedir=${prefix}/include/fastahack~@
+ ~@
+ ~@
+ Name: fastahack~@
+ Version: ~a~@
+ Description: Indexing and sequence extraction from FASTA files~@
+ Libs: -L${libdir} -lfastahack~@
+ Cflags: -I${includedir}~%"
+ out ,version))))
#t)))))
(home-page "https://github.com/ekg/fastahack")
(synopsis "Indexing and sequence extraction from FASTA files")
"/vcflib-" version "-src.tar.gz"))
(sha256
(base32 "14zzrg8hg8cq9cvq2wdvp21j7nmxxkjrbagw2apd2yqv2kyx42lm"))
+ (patches (search-patches "vcflib-use-shared-libraries.patch"))
(modules '((guix build utils)))
(snippet
`(begin
+ (substitute* (find-files "." "\\.(h|c)(pp)?$")
+ (("\"SmithWatermanGotoh.h\"") "<smithwaterman/SmithWatermanGotoh.h>")
+ (("\"convert.h\"") "<smithwaterman/convert.h>")
+ (("\"disorder.h\"") "<smithwaterman/disorder.h>")
+ (("\"tabix.hpp\"") "<tabix.hpp>")
+ (("\"Fasta.h\"") "<fastahack/Fasta.h>"))
(for-each delete-file-recursively
'("fastahack" "filevercmp" "fsom" "googletest" "intervaltree"
"libVCFH" "multichoose" "smithwaterman" "tabixpp"))
(build-system gnu-build-system)
(inputs
`(("htslib" ,htslib)
+ ("fastahack" ,fastahack)
("perl" ,perl)
("python" ,python)
+ ("smithwaterman" ,smithwaterman)
+ ("tabixpp" ,tabixpp)
+ ("xz" ,xz)
("zlib" ,zlib)))
(native-inputs
- `(;; Submodules.
+ `(("pkg-config" ,pkg-config)
+ ;; Submodules.
;; This package builds against the .o files so we need to extract the source.
- ("fastahack-src" ,(package-source fastahack))
("filevercmp-src" ,(package-source filevercmp))
- ("fsom-src" ,(package-source fsom))
("intervaltree-src" ,(package-source intervaltree))
- ("multichoose-src" ,(package-source multichoose))
- ("smithwaterman-src" ,(package-source smithwaterman))
- ("tabixpp-src" ,(package-source tabixpp))))
+ ("multichoose-src" ,(package-source multichoose))))
(arguments
`(#:tests? #f ; no tests
- #:make-flags (list (string-append "HTS_LIB="
- (assoc-ref %build-inputs "htslib")
- "/lib/libhts.a")
- (string-append "HTS_INCLUDES= -I"
- (assoc-ref %build-inputs "htslib")
- "/include/htslib")
- (string-append "HTS_LDFLAGS= -L"
- (assoc-ref %build-inputs "htslib")
- "/include/htslib" " -lhts"))
#:phases
(modify-phases %standard-phases
+ (add-after 'unpack 'set-flags
+ (lambda* (#:key outputs #:allow-other-keys)
+ (substitute* "Makefile"
+ (("LDFLAGS =")
+ (string-append "LDFLAGS = -Wl,-rpath="
+ (assoc-ref outputs "out") "/lib ")))
+ (substitute* "filevercmp/Makefile"
+ (("-c") "-c -fPIC"))
+ #t))
(delete 'configure)
- (delete 'check)
(add-after 'unpack 'unpack-submodule-sources
(lambda* (#:key inputs #:allow-other-keys)
(let ((unpack (lambda (source target)
(assoc-ref inputs source)
"--strip-components=1"))))))
(and
- (unpack "fastahack-src" "fastahack")
(unpack "filevercmp-src" "filevercmp")
- (unpack "fsom-src" "fsom")
(unpack "intervaltree-src" "intervaltree")
- (unpack "multichoose-src" "multichoose")
- (unpack "smithwaterman-src" "smithwaterman")
- (unpack "tabixpp-src" "tabixpp")))))
- (replace 'build
- (lambda* (#:key inputs make-flags #:allow-other-keys)
- (let ((htslib (assoc-ref inputs "htslib")))
- (with-directory-excursion "tabixpp"
- (substitute* "Makefile"
- (("-Ihtslib") (string-append "-I" htslib "/include/htslib"))
- (("-Lhtslib") (string-append "-L" htslib "/lib/htslib"))
- (("htslib/htslib") (string-append htslib "/include/htslib")))
- (invoke "make"
- (string-append "HTS_LIB=" htslib "/lib/libhts.a")))
- (apply invoke "make" "CC=gcc" "CFLAGS=-Itabixpp" make-flags))))
+ (unpack "multichoose-src" "multichoose")))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
- (lib (string-append (assoc-ref outputs "out") "/lib")))
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (lib (string-append out "/lib")))
(for-each (lambda (file)
(install-file file bin))
(find-files "bin" ".*"))
- ;; The header files in src/ do not interface libvcflib,
- ;; therefore they are left out.
- (install-file "libvcflib.a" lib))
+ (install-file "libvcflib.so" lib)
+ (install-file "libvcflib.a" lib)
+ (for-each
+ (lambda (file)
+ (install-file file (string-append out "/include")))
+ (find-files "include" "\\.h(pp)?$"))
+ (mkdir-p (string-append lib "/pkgconfig"))
+ (with-output-to-file (string-append lib "/pkgconfig/vcflib.pc")
+ (lambda _
+ (format #t "prefix=~a~@
+ exec_prefix=${prefix}~@
+ libdir=${exec_prefix}/lib~@
+ includedir=${prefix}/include~@
+ ~@
+ ~@
+ Name: libvcflib~@
+ Version: ~a~@
+ Requires: smithwaterman, fastahack~@
+ Description: C++ library for parsing and manipulating VCF files~@
+ Libs: -L${libdir} -lvcflib~@
+ Cflags: -I${includedir}~%"
+ out ,version))))
#t)))))
(home-page "https://github.com/vcflib/vcflib/")
(synopsis "Library for parsing and manipulating VCF files")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ekg/freebayes.git")
+ (url "https://github.com/ekg/freebayes")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/GregoryFaust/samblaster.git")
+ (url "https://github.com/GregoryFaust/samblaster")
(commit (string-append "v." version))))
(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/velocyto-team/velocyto.R.git")
+ (url "https://github.com/velocyto-team/velocyto.R")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/dpryan79/MethylDackel.git")
+ (url "https://github.com/dpryan79/MethylDackel")
(commit version)))
(file-name (git-file-name name version))
(sha256
;; See https://github.com/dpryan79/MethylDackel/issues/85
(license license:expat)))
+;; This package bundles PCRE 8.02 and cannot be built with the current
+;; version.
+(define-public phast
+ (package
+ (name "phast")
+ (version "1.5")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/CshlSiepelLab/phast")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "10lpbllvny923jjbbyrpxahhd1m5h7sbj9gx7rd123rg10mlidki"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:make-flags
+ (list "CC=gcc"
+ (string-append "DESTDIR=" (assoc-ref %outputs "out")))
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'configure
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ ;; Fix syntax
+ (substitute* "test/Makefile"
+ ((" ") " "))
+ (substitute* "Makefile"
+ (("CLAPACKPATH=/usr/lib")
+ (string-append "CLAPACKPATH="
+ (assoc-ref inputs "clapack") "/lib")))
+ ;; Renaming the libraries is not necessary with our version of
+ ;; CLAPACK.
+ (substitute* "src/lib/Makefile"
+ (("ifdef CLAPACKPATH") "ifdef UNNECESSARY"))
+ (substitute* "src/make-include.mk"
+ (("-lblaswr") "-lblas")
+ (("-ltmg") "-ltmglib")
+ (("liblapack.a") "liblapack.so")
+ (("libblas.a") "libblas.so")
+ (("libf2c.a") "libf2c.so"))
+ (substitute* "src/Makefile"
+ (("/opt") "/share")
+ (("/usr/") "/"))
+ #t))
+ (replace 'check
+ (lambda _
+ (setenv "PATH"
+ (string-append (getcwd) "/bin:" (getenv "PATH")))
+ ;; Disable broken test
+ (substitute* "test/Makefile"
+ ((".*if.*hmrc_summary" m) (string-append "#" m)))
+ ;; Only run the msa_view tests because the others fail for
+ ;; unknown reasons.
+ (invoke "make" "-C" "test" "msa_view"))))))
+ (inputs
+ `(("clapack" ,clapack)))
+ (native-inputs
+ `(("perl" ,perl)))
+ (home-page "http://compgen.cshl.edu/phast/")
+ (synopsis "Phylogenetic analysis with space/time models")
+ (description
+ "Phylogenetic Analysis with Space/Time models (PHAST) is a collection of
+command-line programs and supporting libraries for comparative and
+evolutionary genomics. Best known as the search engine behind the
+Conservation tracks in the University of California, Santa Cruz (UCSC) Genome
+Browser, PHAST also includes several tools for phylogenetic modeling,
+functional element identification, as well as utilities for manipulating
+alignments, trees and genomic annotations.")
+ (license license:bsd-3)))
+
(define-public python-gffutils
;; The latest release is older more than a year than the latest commit
(let ((commit "4034c54600813b1402945e12faa91b3a53162cf1")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/daler/gffutils.git")
+ (url "https://github.com/daler/gffutils")
(commit commit)))
(file-name (git-file-name name version))
(sha256
HCoop / jackhill / guix / guix.git / blobdiff