diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 92 |
1 files changed, 92 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5fbfdf0b9b..43faaa078f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -56,6 +56,8 @@ #:use-module (gnu packages gtk) #:use-module (gnu packages glib) #:use-module (gnu packages groff) + #:use-module (gnu packages guile) + #:use-module (gnu packages haskell) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) #:use-module (gnu packages java) @@ -7137,6 +7139,96 @@ ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.") (license license:gpl2+))) +(define-public r-rcas + (package + (name "r-rcas") + (version "0.99.6") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/BIMSBbioinfo/RCAS/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1ljgl2b4r6w2n0i9i04d9xaphajsvhfkjdj2i2z830nha4m3w8f0")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr) + ("r-testthat" ,r-testthat) + ;; During vignette building knitr checks that "pandoc-citeproc" + ;; is in the PATH. + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc))) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-biomart" ,r-biomart) + ("r-org-hs-eg-db" ,r-org-hs-eg-db) + ("r-org-ce-eg-db" ,r-org-ce-eg-db) + ("r-org-dm-eg-db" ,r-org-dm-eg-db) + ("r-org-mm-eg-db" ,r-org-mm-eg-db) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) + ("r-bsgenome-celegans-ucsc-ce10" ,r-bsgenome-celegans-ucsc-ce10) + ("r-bsgenome-dmelanogaster-ucsc-dm3" ,r-bsgenome-dmelanogaster-ucsc-dm3) + ("r-topgo" ,r-topgo) + ("r-dt" ,r-dt) + ("r-plotly" ,r-plotly) + ("r-motifrg" ,r-motifrg) + ("r-genomation" ,r-genomation) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-rtracklayer" ,r-rtracklayer) + ("r-rmarkdown" ,r-rmarkdown))) + (synopsis "RNA-centric annotation system") + (description + "RCAS aims to be a standalone RNA-centric annotation system that provides +intuitive reports and publication-ready graphics. This package provides the R +library implementing most of the pipeline's features.") + (home-page "https://github.com/BIMSBbioinfo/RCAS") + (license license:expat))) + +(define-public rcas-web + (package + (name "rcas-web") + (version "0.0.3") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/BIMSBbioinfo/rcas-web/" + "releases/download/v" version + "/rcas-web-" version ".tar.gz")) + (sha256 + (base32 + "0d3my0g8i7js59n184zzzjdki7hgmhpi4rhfvk7i6jsw01ba04qq")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'install 'wrap-executable + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (json (assoc-ref inputs "guile-json")) + (redis (assoc-ref inputs "guile-redis")) + (path (string-append + json "/share/guile/site/2.2:" + redis "/share/guile/site/2.2"))) + (wrap-program (string-append out "/bin/rcas-web") + `("GUILE_LOAD_PATH" ":" = (,path)) + `("GUILE_LOAD_COMPILED_PATH" ":" = (,path)) + `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))))) + #t))))) + (inputs + `(("r" ,r) + ("r-rcas" ,r-rcas) + ("guile-next" ,guile-next) + ("guile-json" ,guile2.2-json) + ("guile-redis" ,guile2.2-redis))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "https://github.com/BIMSBbioinfo/rcas-web") + (synopsis "Web interface for RNA-centric annotation system (RCAS)") + (description "This package provides a simple web interface for the +@dfn{RNA-centric annotation system} (RCAS).") + (license license:agpl3+))) + (define-public emboss (package (name "emboss") |