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| author | Ricardo Wurmus <rekado@elephly.net> | 2023-11-03 19:08:19 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2023-11-03 22:49:28 +0100 |
| commit | abaca151b2aaf1c6e8d05afed9e14daa9259c66c (patch) | |
| tree | 1d00848a2de822941b14e5380dcc2547da55d542 | |
| parent | b30127052ecbf581f83bcf18c571bc7cdea52364 (diff) | |
gnu: r-mpo-db: Include HPO sqlite database.
* gnu/packages/bioconductor.scm (r-mpo-db)[arguments]: Bypass fetching of the
database from the internet when in build environment.
[native-inputs]: Add MPO.sqlite.
Change-Id: Ic7228322b89ce78a85a9bd5ffbd985ccd906d268
| -rw-r--r-- | gnu/packages/bioconductor.scm | 28 |
1 files changed, 27 insertions, 1 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1729066a10..8f95fd7e5c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -164,9 +164,35 @@ It retrieves this data from the Genome Aggregation Database (base32 "0x1rcikg189akbd71yh0p02482km9hry6i69s2srdf5mlgqficvl")))) (properties `((upstream-name . "MPO.db"))) (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'avoid-internet-access + (lambda* (#:key inputs #:allow-other-keys) + (let* ((cache (string-append #$output "/share/MPO.db/cache")) + (file (string-append cache "/118299"))) + (mkdir-p cache) + (copy-file #$(this-package-native-input "MPO.sqlite") file) + (substitute* "R/zzz.R" + (("ah <- suppressMessages\\(AnnotationHub\\(\\)\\)" m) + (string-append + "if (Sys.getenv(\"NIX_BUILD_TOP\") == \"\") { " m " };")) + (("dbfile <- ah.*" m) + (string-append + "if (Sys.getenv(\"NIX_BUILD_TOP\") != \"\") { dbfile <- \"" + file "\";} else { " m " }\n"))))))))) (propagated-inputs (list r-annotationdbi r-annotationhub r-biocfilecache r-dbi)) - (native-inputs (list r-knitr)) + (native-inputs + `(("r-knitr" ,r-knitr) + ("MPO.sqlite" + ,(origin + (method url-fetch) + (uri "https://annotationhub.bioconductor.org/fetch/118299") + (file-name "MPO.sqlite") + (sha256 + (base32 "12rf5dpnjrpw55bgnbn68dni2g0p87nvs9c7mamqk0ayafs61zl0")))))) (home-page "https://github.com/YuLab-SMU/MPO.db") (synopsis "set of annotation maps describing the Mouse Phenotype Ontology") (description |