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gnu: r-variantfiltering: Add missing inputs.

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* gnu/packages/bioconductor.scm (r-variantfiltering)[native-inputs]: Add
r-biocstyle, r-bsgenome-hsapiens-1000genomes-hs37d5, r-org-hs-eg-db, and
r-txdb-hsapiens-ucsc-hg19-knowngene.
[properties]: Tell updater to keep extra inputs.
[arguments]: Add phase 'delete-bad-tests; disable vignettes.

Change-Id: I23e78f1bd49b348719c6e03a116228b5657ae379
This commit is contained in:
Ricardo Wurmus 2024-11-29 09:19:49 +01:00
parent 8dd751f114
commit 18c5a3b324
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GPG key ID: 197A5888235FACAC
1 changed files with 24 additions and 2 deletions
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26
gnu/packages/bioconductor.scm
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@ -21457,8 +21457,25 @@ provides methods for retrieving enriched pathways.")
(base32
"0839ljb4fh1qrjk1xm89q2hwnbbxi2slaw3l36dk8kmpifhqqi16"))))
(properties
`((upstream-name . "VariantFiltering")))
`((upstream-name . "VariantFiltering")
(updater-extra-native-inputs
. ("r-biocstyle"
"r-bsgenome-hsapiens-1000genomes-hs37d5"
"r-org-hs-eg-db"
"r-txdb-hsapiens-ucsc-hg19-knowngene"))))
(build-system r-build-system)
(arguments
(list
;; Vignettes require an obscene amount of humongous annotation packages
;; and *still* attempt to download additional files off the Internet.
;; Enough is enough.
#:test-types '(list "tests")
#:phases
'(modify-phases %standard-phases
(add-after 'unpack 'delete-bad-tests
(lambda _
;; One test tries to connect to a website.
(delete-file "inst/unitTests/test_location-methods.R"))))))
(propagated-inputs
(list r-annotationdbi
r-biobase
@ -21484,7 +21501,12 @@ provides methods for retrieving enriched pathways.")
r-summarizedexperiment
r-variantannotation
r-xvector))
(native-inputs (list r-runit))
(native-inputs
(list r-biocstyle
r-bsgenome-hsapiens-1000genomes-hs37d5
r-org-hs-eg-db
r-runit
r-txdb-hsapiens-ucsc-hg19-knowngene))
(home-page "https://github.com/rcastelo/VariantFiltering")
(synopsis "Filtering of coding and non-coding genetic variants")
(description