;;; 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
(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")
(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
(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
(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
(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 "1.56.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biocViews" version))
(sha256
(base32
- "1h4cmfbff79v9xrh271dp3rv0877ris06lmkvc39kqzj7yjsh7c2"))))
+ "0zcx8gha3x3jc0ra6ii6wwq2vfsmffrrnilknbq8h5xjrl55m6ci"))))
(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 "1.50.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationDbi" version))
(sha256
(base32
- "10gplxal0qphcn29azv0i6hiim9q45lmhzvhhhsnwfhwpgja7p05"))))
+ "00pd8lsdppxlmx0l65phw0jhsm0qkwjc4wsdxpvgc31iiz9yslbj"))))
(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-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
(define-public r-qtl2
(package
(name "r-qtl2")
- (version "0.20")
+ (version "0.22-11")
(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"))))
+ (method url-fetch)
+ (uri (cran-uri "qtl2" version))
+ (sha256
+ (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr"))))
(build-system r-build-system)
(propagated-inputs
`(("r-data-table" ,r-data-table)
("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")
+ (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
(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.")
+ "This package provides a set of tools to perform @dfn{Quantitative Trait
+Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
+@code{R/qtl} package to better handle high-dimensional data and complex cross
+designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
(license license:gpl3)))
(define-public r-zlibbioc
(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))
(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
(define-public r-msnid
(package
(name "r-msnid")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MSnID" version))
(sha256
(base32
- "0m71f2y12hmwvng45kzz4r4qrgc2jbd7j9gprmw8y5laawpdaifg"))))
+ "0dwa6j2nqb3223a8g4f453aznjh69wngrpvdi12iy69j1psbbjcc"))))
(properties `((upstream-name . "MSnID")))
(build-system r-build-system)
(propagated-inputs
(define-public r-aroma-light
(package
(name "r-aroma-light")
- (version "3.16.0")
+ (version "3.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "aroma.light" version))
(sha256
(base32
- "0cgdg650j4dl0b45pwaw49ib97dwjazrv9sqzkygrjmcnnfxry8x"))))
+ "19y5f2minx2pp73zdh43v1qkwpkaxygkl8cwlnwja15i46s0bcyc"))))
(properties `((upstream-name . "aroma.light")))
(build-system r-build-system)
(propagated-inputs
(define-public r-deseq
(package
(name "r-deseq")
- (version "1.38.0")
+ (version "1.39.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DESeq" version))
(sha256
(base32
- "14pys93gsl50xmq5pc7pp1g20v3ywlg0yzkkhwb3kiy8573xn9nc"))))
+ "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1"))))
(properties `((upstream-name . "DESeq")))
(build-system r-build-system)
(propagated-inputs
(define-public r-edaseq
(package
(name "r-edaseq")
- (version "2.20.0")
+ (version "2.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "EDASeq" version))
(sha256
(base32
- "19mgzbv8yxgvw86wpq401l27q55ygawlngl775yavwccz1zbhjnj"))))
+ "12gzxjh73qshlwvsf92lbrf4bi199kxg2snrkprh1z4yqf7bjfm4"))))
(properties `((upstream-name . "EDASeq")))
(build-system r-build-system)
(propagated-inputs
("r-iranges" ,r-iranges)
("r-rsamtools" ,r-rsamtools)
("r-shortread" ,r-shortread)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/drisso/EDASeq")
(synopsis "Exploratory data analysis and normalization for RNA-Seq")
(description
(define-public r-interactivedisplaybase
(package
(name "r-interactivedisplaybase")
- (version "1.24.0")
+ (version "1.26.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "interactiveDisplayBase" version))
(sha256
(base32
- "0zwf3ma6wf4zypl6bgjp0n72k2hmp0g16gzl4v3y4157rxcbpl0n"))))
+ "1x5vipqa4pgwpd62c1c58shnlpv3zyzzpf4wdwr00q1swkdb7wv3"))))
(properties
`((upstream-name . "interactiveDisplayBase")))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
+ ("r-dt" ,r-dt)
("r-shiny" ,r-shiny)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/interactiveDisplayBase")
(synopsis "Base package for web displays of Bioconductor objects")
(description
(define-public r-annotationhub
(package
(name "r-annotationhub")
- (version "2.18.0")
+ (version "2.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationHub" version))
(sha256
(base32
- "19vj3bk8jz68q84g3j8xs1s9bqz90lbwbciig1h45zvn2zc6087m"))))
+ "0r4xzf93bm9cpys5cg70wg0b8hxli80hvqwgh4hzbd45yyf5c4wz"))))
(properties `((upstream-name . "AnnotationHub")))
(build-system r-build-system)
(propagated-inputs
("r-rsqlite" ,r-rsqlite)
("r-s4vectors" ,r-s4vectors)
("r-yaml" ,r-yaml)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/AnnotationHub")
(synopsis "Client to access AnnotationHub resources")
(description
(define-public r-fastseg
(package
(name "r-fastseg")
- (version "1.32.0")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "fastseg" version))
(sha256
(base32
- "1cys6frmbizc8bf933mwvvnr31sfya9ahcc0wm66pbd1x3mygkmk"))))
+ "1d48n245pzmvcpsz93lxb4frqh222gfhpmlvm0sb74skn16way63"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
(define-public r-keggrest
(package
(name "r-keggrest")
- (version "1.26.1")
+ (version "1.28.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "KEGGREST" version))
(sha256
(base32
- "1cgjvv9n88y3ah21356mh8z2l08vjn42hjy8hcljsibknzc4v247"))))
+ "0q76w17fya2x0z7mvyhkk5kqh07flldgih13ma44vhcy1bdlm6j1"))))
(properties `((upstream-name . "KEGGREST")))
(build-system r-build-system)
(propagated-inputs
`(("r-biostrings" ,r-biostrings)
("r-httr" ,r-httr)
("r-png" ,r-png)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/KEGGREST")
(synopsis "Client-side REST access to KEGG")
(description
(define-public r-gage
(package
(name "r-gage")
- (version "2.36.0")
+ (version "2.37.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gage" version))
(sha256
(base32
- "1qxfmg0id19iy3ia8h5nrvk3d1azqb28kl7m08i23654wb6b45c6"))))
+ "1zfaas4x6g7wiml6cmxa7b4f43az9s0lrw80k6sf7c96hsh1jijr"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
(define-public r-genomicfiles
(package
(name "r-genomicfiles")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFiles" version))
(sha256
(base32
- "1x6q827ms2l5lwzha1vsgfrshh35n9f19jq57xagrqlafxgpz86s"))))
+ "1k3824pzf9fdqvcv6cz2742q3mabpmncrc72hwa21ac8wy1b04n4"))))
(properties `((upstream-name . "GenomicFiles")))
(build-system r-build-system)
(propagated-inputs
(define-public r-complexheatmap
(package
(name "r-complexheatmap")
- (version "2.2.0")
+ (version "2.4.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ComplexHeatmap" version))
(sha256
(base32
- "1pj6a6rmqckk033pkklk6hr4066rzavamy6w194rfdhind90rk0p"))))
+ "01jxxwxhf9n8baxgja4rb592p5210s4ppd7a5b4xby5aalhzkr0l"))))
(properties
`((upstream-name . "ComplexHeatmap")))
(build-system r-build-system)
("r-globaloptions" ,r-globaloptions)
("r-png" ,r-png)
("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page
"https://github.com/jokergoo/ComplexHeatmap")
(synopsis "Making Complex Heatmaps")
(define-public r-dirichletmultinomial
(package
(name "r-dirichletmultinomial")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DirichletMultinomial" version))
(sha256
(base32
- "0knmncmkkf2ypyqfcl5s8nmyyf9nrzkqprzn9w3w8182c0v49r0s"))))
+ "1m9dsrddrllb2i88qzik1867iv9mggrgdkn0dlp8sq7gl69vmalb"))))
(properties
`((upstream-name . "DirichletMultinomial")))
(build-system r-build-system)
(define-public r-ensembldb
(package
(name "r-ensembldb")
- (version "2.10.2")
+ (version "2.12.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ensembldb" version))
(sha256
(base32
- "02lnpyp85zchmz404hr5381zmihvq4x9zgxdrbn2afi352vg0vab"))))
+ "1vvchc04nshxc768fp31rxb603aj3hmq8xlh5qabcwf2c3z9719g"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-rsqlite" ,r-rsqlite)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/jotsetung/ensembldb")
(synopsis "Utilities to create and use Ensembl-based annotation databases")
(description
(define-public r-organismdbi
(package
(name "r-organismdbi")
- (version "1.28.0")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "OrganismDbi" version))
(sha256
(base32
- "1bvfyh733mhka9zd00hrzpalgjs255c2blnxyf60ipzk5jg7yllb"))))
+ "194h5576inq44qr666snzq0ygnc77rk5ljkn9bn8zs6x6gb3cwaw"))))
(properties `((upstream-name . "OrganismDbi")))
(build-system r-build-system)
(propagated-inputs
(define-public r-biovizbase
(package
(name "r-biovizbase")
- (version "1.34.1")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biovizBase" version))
(sha256
(base32
- "04vvj907bgs67w8rb7n1haf80p6cd0qj5fdxw0dwryb455y35vir"))))
+ "1vq2mxa2jkljgw75zqjdkyml0ppi5dspvwj4cznfhi31cq8ds0qh"))))
(properties `((upstream-name . "biovizBase")))
(build-system r-build-system)
(propagated-inputs
(define-public r-ggbio
(package
(name "r-ggbio")
- (version "1.34.0")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ggbio" version))
(sha256
(base32
- "13wzwh40anh8l53yp19bg4w5cpxykcaf228dc8cxvjndyib711qb"))))
+ "11ggnqjq42fi2hm9xlvrrlr2xhy4kglvl1a0mycp1s4v67lxw5h5"))))
(build-system r-build-system)
(arguments
`(#:phases
("r-scales" ,r-scales)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-variantannotation" ,r-variantannotation)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "http://www.tengfei.name/ggbio/")
(synopsis "Visualization tools for genomic data")
(description
(define-public r-gqtlbase
(package
(name "r-gqtlbase")
- (version "1.18.0")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gQTLBase" version))
(sha256
(base32
- "1qr8dqjbmj1mdjbzbnxwzfrm8f02wqfsgic8ws5kv7pmsby63y4x"))))
+ "06xvzp4fn3qfa46ggg8kxi267gbyd821vvx4040173xkqxpr0g5j"))))
(properties `((upstream-name . "gQTLBase")))
(build-system r-build-system)
(propagated-inputs
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)
("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/gQTLBase")
(synopsis "Infrastructure for eQTL, mQTL and similar studies")
(description
(define-public r-snpstats
(package
(name "r-snpstats")
- (version "1.36.0")
+ (version "1.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "snpStats" version))
(sha256
(base32
- "1xq1rjljg70h5mshdza56dis0iv1a20sivs6dav3w5jbdd1l5qkh"))))
+ "1qv3nqqr30d3n66mawqd9dbl95dl89r4bcjvkc5iassy1yrwr8wq"))))
(properties `((upstream-name . "snpStats")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
(define-public r-erma
(package
(name "r-erma")
- (version "1.2.0")
+ (version "1.4.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "erma" version))
(sha256
(base32
- "085qsr73p8nyp435f15l4l1jkfd64bfd9gl4z496nfxdnqn95srz"))))
+ "1ccfbq0r48sr3h8050w8zv8402h7nx09adr0xdyqlg7kwp9vd2l3"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-s4vectors" ,r-s4vectors)
("r-shiny" ,r-shiny)
("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/erma")
(synopsis "Epigenomic road map adventures")
(description
(define-public r-ldblock
(package
(name "r-ldblock")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ldblock" version))
(sha256
(base32
- "0xpigfidmylfawy6vzshqnsw1lzjs4qms8q7zffij6bkvkv7920x"))))
+ "0plw00n2zfgh029ab41dnydzgv2yxrapjp770147rx9pff4dngrv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-rsamtools" ,r-rsamtools)
("r-snpstats" ,r-snpstats)
("r-variantannotation" ,r-variantannotation)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/ldblock")
(synopsis "Data structures for linkage disequilibrium measures in populations")
(description
(define-public r-gqtlstats
(package
(name "r-gqtlstats")
- (version "1.18.0")
+ (version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gQTLstats" version))
(sha256
(base32
- "1dly4p9r4231hf31xg1nzqiyvjbcfjljfmhb88ic1jxwnvniyv2f"))))
+ "1jjqfpjp93nmxjn757j5mzcax96bzcqdd1gr3rsdxg7ap008l2w7"))))
(properties `((upstream-name . "gQTLstats")))
(build-system r-build-system)
(propagated-inputs
("r-snpstats" ,r-snpstats)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-variantannotation" ,r-variantannotation)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/gQTLstats")
(synopsis "Computationally efficient analysis for eQTL and allied studies")
(description
(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
(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")
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(file-name (git-file-name name version))
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(method git-fetch)
(uri (git-reference
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(sha256
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(sha256
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(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
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(native-inputs
`(("java-junit" ,java-junit)
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(synopsis "Biojava interface to the forester phylogenomics library")
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(native-inputs
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(native-inputs
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(native-inputs
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("python-wrapper" ,python-wrapper)
("python-pyyaml" ,python-pyyaml)))
- (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
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("kentutils" ,kentutils)))
(native-inputs
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+ (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
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("trim-galore" ,trim-galore)
("cutadapt" ,cutadapt)
("samtools" ,samtools)))
- (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
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(synopsis "Bisulfite sequencing pipeline from fastq to methylation reports")
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("r-stringr" ,r-stringr)
("r-yaml" ,r-yaml)))
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+ (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
(synopsis "Analysis pipeline for single-cell RNA sequencing experiments")
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("pigx-scrnaseq" ,pigx-scrnaseq)))
- (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
+ (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
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following pipelines:
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(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(install-file "miniasm" bin)
- (install-file "minidot" bin)))))))
+ (install-file "minidot" bin)
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