diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2024-11-29 11:50:45 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2024-12-03 16:59:58 +0100 |
| commit | 1c559a129c0c62fb1a52235965198557695e0790 (patch) | |
| tree | de1c5fc92805fab567e60ee6e6022955fdea4d25 /gnu/packages/bioconductor.scm | |
| parent | d09ff90cb681b3953f20e2b4555a60b1f6b1fd18 (diff) | |
gnu: r-rnbeads: Add missing inputs.
* gnu/packages/bioconductor.scm (r-rnbeads)[native-inputs]: Add ghostscript,
r-doparallel, r-impute, r-missmethyl, r-qvalue, r-rnbeads-hg19, and
r-rtracklayer.
[inputs]: Add kentutils.
[source]: Add snippet to delete bundled binaries.
[arguments]: Add phase 'link-to-executables; disable vignettes.
[properties]: Tell updater what inputs to ignore and what to keep.
[description]: Reflow paragraph.
Change-Id: Ied81eeee2210fac43c3868d268aa20c1d0a0fb50
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 42 |
1 files changed, 37 insertions, 5 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7f2d81dd41..a85aaf7005 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9822,9 +9822,32 @@ of other R packages who wish to make use of HTSlib.") (method url-fetch) (uri (bioconductor-uri "RnBeads" version)) (sha256 - (base32 "006kmfg1lysa9z9cbc507l54xh1apslrxxk41w65zp7bqkhs2zj9")))) - (properties `((upstream-name . "RnBeads"))) + (base32 "006kmfg1lysa9z9cbc507l54xh1apslrxxk41w65zp7bqkhs2zj9")) + (modules '((guix build utils))) + (snippet + '(delete-file-recursively "inst/bin")))) + (properties + `((upstream-name . "RnBeads") + (updater-extra-inputs . ("kentutils")) + (updater-extra-native-inputs + . ("r-impute" "r-missmethyl" "r-doparallel" "r-qvalue" "ghostscript")))) (build-system r-build-system) + (arguments + (list + ;; Vignette ‘RnBeads.Rnw’ overwrites the following ‘tangle’ output by + ;; vignette ‘RnBeads_Annotations.Rnw’: RnBeads_Annotations.R + #:test-types '(list "tests") + #:phases + #~(modify-phases %standard-phases + (add-after 'install 'link-to-executables + (lambda* (#:key inputs #:allow-other-keys) + (let ((bin (string-append #$output + "/site-library/RnBeads/bin/linux_x86.64"))) + (mkdir-p bin) + (symlink (search-input-file inputs "/bin/bedToBigBed") + (string-append bin "/bedToBigBed")) + (symlink (search-input-file inputs "/bin/bedGraphToBigWig") + (string-append bin "/bedGraphToBigWig")))))))) (propagated-inputs (list r-biocgenerics r-cluster @@ -9842,12 +9865,21 @@ of other R packages who wish to make use of HTSlib.") r-methylumi r-plyr r-s4vectors)) - (native-inputs (list r-runit)) + (inputs (list kentutils)) + (native-inputs + (list ghostscript + r-doparallel + r-impute + r-missmethyl + r-qvalue + r-rnbeads-hg19 + r-rtracklayer + r-runit)) (home-page "https://bioconductor.org/packages/RnBeads") (synopsis "RnBeads") (description - "@code{RnBeads} facilitates comprehensive analysis of various types of DNA -methylation data at the genome scale.") + "@code{RnBeads} facilitates comprehensive analysis of various types of +DNA methylation data at the genome scale.") (license license:gpl3))) (define-public r-impute |