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author | Ricardo Wurmus <rekado@elephly.net> | 2022-08-10 15:37:55 +0200 |
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committer | Ricardo Wurmus <rekado@elephly.net> | 2022-08-10 15:44:28 +0200 |
commit | fd4b8e987313644dd63717da17ef16e8e18b7f3f (patch) | |
tree | 2e61107b248880192fd8124750da6e5f71dd0dbf /gnu/packages/bioinformatics.scm | |
parent | ee30369c47ca7acbe698aed91d2b0e8a0f1a9fc0 (diff) | |
download | guix-fd4b8e987313644dd63717da17ef16e8e18b7f3f.tar.gz guix-fd4b8e987313644dd63717da17ef16e8e18b7f3f.zip |
gnu: Add r-omnipathr/devel.
* gnu/packages/bioinformatics.scm (r-omnipathr/devel): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r-- | gnu/packages/bioinformatics.scm | 65 |
1 files changed, 65 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3a40cc2281..aae25379fd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11535,6 +11535,71 @@ including: dynamic cellular processes at single-cell resolution.") (license license:expat)))) +;; Needed for r-liana +(define-public r-omnipathr/devel + (let ((commit "679bb79e319af246a16968d27d64d8d6937a331a") + (revision "1")) + (package + (name "r-omnipathr") + (version (git-version "3.5.5" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/saezlab/omnipathr") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "10h6lyapyx4ik8r4kx5z2dly46jlf2v57caq4g6i0hzifyz2vgjq")))) + (properties `((upstream-name . "OmnipathR"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) + (propagated-inputs + (list r-checkmate + r-crayon + r-curl + r-digest + r-dplyr + r-httr + r-igraph + r-jsonlite + r-later + r-logger + r-magrittr + r-progress + r-purrr + r-rappdirs + r-readr + r-readxl + r-rlang + r-rvest + r-stringr + r-tibble + r-tidyr + r-tidyselect + r-withr + r-xml2 + r-yaml)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/saezlab/omnipathr") + (synopsis "OmniPath web service client and more") + (description + "This package provides a client for the OmniPath web service and many +other resources. It also includes functions to transform and pretty print +some of the downloaded data, functions to access a number of other resources +such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to +Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, +InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, +RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, +OmnipathR features a close integration with the NicheNet method for ligand +activity prediction from transcriptomics data, and its R implementation +@code{nichenetr}.") + (license license:expat)))) + (define-public r-circus (package (name "r-circus") |