diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2023-11-03 19:05:57 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2023-11-03 22:49:28 +0100 |
| commit | c66c66ee3fd02d03679e59dc69c05fd6597e4d86 (patch) | |
| tree | 6033ff1c358dd1a01cd1c09dba67fc94032f12a0 | |
| parent | a9383428994dbe1b3266bfe020aba3c31e3a75f4 (diff) | |
gnu: r-hpo-db: Include HPO sqlite database.
* gnu/packages/bioconductor.scm (r-hpo-db)[arguments]: Bypass fetching of the
database from the internet when in build environment.
[native-inputs]: Add HPO.sqlite.
Change-Id: Ie01605ef2531d992fb85c07bae5cfaabda626ea6
| -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 18d24784b2..1729066a10 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -81,9 +81,35 @@ (base32 "1brzrnafvyh76h8a663gk5lprhixxpi9xi65vwgxwf7jh6yw0was")))) (properties `((upstream-name . "HPO.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 #$output "/share/HPO.db/cache")) + (file (string-append cache "/118333"))) + (mkdir-p cache) + (copy-file #$(this-package-native-input "HPO.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) + ("HPO.sqlite" + ,(origin + (method url-fetch) + (uri "https://annotationhub.bioconductor.org/fetch/118333") + (file-name "HPO.sqlite") + (sha256 + (base32 "1wwdwf27iil0p41183qgygh2ifphhmlljjkgjm2h8sr25qycf0md")))))) (home-page "https://bioconductor.org/packages/HPO.db") (synopsis "Annotation maps describing the entire Human Phenotype Ontology") |