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03/03: gnu: r-mpo-db: Include HPO sqlite database.
From: |
guix-commits |
Subject: |
03/03: gnu: r-mpo-db: Include HPO sqlite database. |
Date: |
Fri, 3 Nov 2023 16:49:54 -0400 (EDT) |
rekado pushed a commit to branch r-updates
in repository guix.
commit 18ca4948a5c1f3e4bddff56dd577b1d24f9bf927
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Fri Nov 3 21:49:18 2023 +0100
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
---
gnu/packages/bioconductor.scm | 37 ++++++++++++++++++++++++-------------
1 file changed, 24 insertions(+), 13 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 85a2b8d087..b15a856fb9 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -167,21 +167,32 @@ It retrieves this data from the Genome Aggregation
Database
(arguments
(list
#:phases
- '(modify-phases %standard-phases
- ;; Needed for annotationhub
- (add-after 'unpack 'set-HOME
- (lambda _
- (setenv "HOME" "/tmp")))
- (add-after 'unpack 'avoid-internet-access
- (lambda _
- (setenv "GUIX_BUILD" "yes")
- (substitute* "R/zzz.R"
- (("ah <- suppressMessages\\(AnnotationHub\\(\\)\\)" m)
- (string-append
- "if (Sys.getenv(\"GUIX_BUILD\") == \"yes\") { return(TRUE);
}; " m))))))))
+ #~(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