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author | Marius Bakke <mbakke@fastmail.com> | 2019-10-18 18:10:47 +0200 |
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committer | Marius Bakke <mbakke@fastmail.com> | 2019-10-18 18:10:47 +0200 |
commit | b95d1b3289a6bb8e346a47e750660e16fb201c57 (patch) | |
tree | cd4d956436f21d77645fd795d3e9737e4892c1d3 /gnu/packages/bioinformatics.scm | |
parent | a1d1703a1dc6bfcd10f48fe707ee7ac65300a37d (diff) | |
parent | dabcfc6de29032ea52d1cb54163a783f7e480167 (diff) | |
download | guix-patches-b95d1b3289a6bb8e346a47e750660e16fb201c57.tar guix-patches-b95d1b3289a6bb8e346a47e750660e16fb201c57.tar.gz |
Merge branch 'master' into staging
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r-- | gnu/packages/bioinformatics.scm | 88 |
1 files changed, 88 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a8662dc238..1e8e357187 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15261,3 +15261,91 @@ and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.") (license license:expat))) + +(define-public r-velocyto + (let ((commit "d7790346cb99f49ab9c2b23ba70dcf9d2c9fc350") + (revision "1")) + (package + (name "r-velocyto") + (version (git-version "0.6" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/velocyto-team/velocyto.R.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "16wqf70j7rd7pay2q513iyz12i8n9vrpg1bisah4lddbcpx5dz1n")))) + (build-system r-build-system) + (inputs + `(("boost" ,boost))) + (propagated-inputs + `(("r-hdf5r" ,r-hdf5r) + ("r-mass" ,r-mass) + ("r-mgcv" ,r-mgcv) + ("r-pcamethods" ,r-pcamethods) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ;; Suggested packages + ("r-rtsne" ,r-rtsne) + ("r-cluster" ,r-cluster) + ("r-abind" ,r-abind) + ("r-h5" ,r-h5) + ("r-biocgenerics" ,r-biocgenerics) + ("r-genomicalignments" ,r-genomicalignments) + ("r-rsamtools" ,r-rsamtools) + ("r-edger" ,r-edger) + ("r-igraph" ,r-igraph))) + (home-page "http://velocyto.org") + (synopsis "RNA velocity estimation in R") + (description + "This package provides basic routines for estimation of gene-specific +transcriptional derivatives and visualization of the resulting velocity +patterns.") + (license license:gpl3)))) + +(define-public methyldackel + (package + (name "methyldackel") + (version "0.4.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dpryan79/MethylDackel.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "10gh8k0ca92kywnrw5pkacq3g6r8s976s12k8jhp8g3g49q9a97g")))) + (build-system gnu-build-system) + (arguments + `(#:test-target "test" + #:make-flags + (list "CC=gcc" + (string-append "prefix=" + (assoc-ref %outputs "out") "/bin/")) + #:phases + (modify-phases %standard-phases + (replace 'configure + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "Makefile" + (("install MethylDackel \\$\\(prefix\\)" match) + (string-append "install -d $(prefix); " match))) + #t))))) + (inputs + `(("htslib" ,htslib) + ("zlib" ,zlib))) + ;; Needed for tests + (native-inputs + `(("python" ,python-wrapper))) + (home-page "https://github.com/dpryan79/MethylDackel") + (synopsis "Universal methylation extractor for BS-seq experiments") + (description + "MethylDackel will process a coordinate-sorted and indexed BAM or CRAM +file containing some form of BS-seq alignments and extract per-base +methylation metrics from them. MethylDackel requires an indexed fasta file +containing the reference genome as well.") + ;; See https://github.com/dpryan79/MethylDackel/issues/85 + (license license:expat))) |