--- Begin Message ---
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Subject: |
[PATCH] gnu: Add r-hdcytodata. |
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Date: |
Fri, 10 Mar 2023 16:16:12 +0000 |
* gnu/packages/bioconductor.scm (r-hdcytodata): New variable.
---
gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d603bd42c1..1cf33501d6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -560,6 +560,46 @@ (define-public r-hdo-db
https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology}.";)
(license license:artistic2.0)))
+(define-public r-hdcytodata
+ (package
+ (name "r-hdcytodata")
+ (version "1.18.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "HDCytoData" version
+ 'experiment))
+ (sha256
+ (base32
+ "1fn8q6ds10z3ymdarkfyh88pcqnrry9yhzammp84vf86f0bl8mrc"))))
+ (properties `((upstream-name . "HDCytoData")))
+ (build-system r-build-system)
+ (arguments
+ (list #:phases '(modify-phases %standard-phases
+ (add-after 'unpack 'set-HOME
+ (lambda _
+ (setenv "HOME" "/tmp")))
+ (add-after 'unpack 'avoid-internet-access
+ (lambda _
+ (setenv "GUIX_BUILD" "yes")
+ (substitute* "R/zzz.R"
+ (("createHubAccessors.*" m)
+ (string-append
+ "if (Sys.getenv(\"GUIX_BUILD\") == \"\") {" m
+ "}"))))))))
+ (propagated-inputs (list r-experimenthub r-flowcore
r-summarizedexperiment))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/lmweber/HDCytoData";)
+ (synopsis
+ "Set of high-dimensional flow cytometry and mass cytometry benchmark
datasets")
+ (description
+ "HDCytoData contains a set of high-dimensional cytometry benchmark
datasets.
+These datasets are formatted into SummarizedExperiment and flowSet
+Bioconductor object formats, including all required metadata. Row metadata
+includes sample IDs, group IDs, patient IDs, reference cell population or
+cluster labels and labels identifying spiked in cells. Column metadata
+includes channel names, protein marker names, and protein marker classes.")
+ (license license:expat)))
+
(define-public r-homo-sapiens
(package
(name "r-homo-sapiens")
--
2.34.1
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--- Begin Message ---
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Subject: |
Re: [bug#62098] [PATCH] gnu: Add r-hdcytodata. |
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Date: |
Sat, 03 Jun 2023 12:15:11 +0100 |
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User-agent: |
mu4e 1.10.2; emacs 28.2 |
Navid Afkhami <navid.afkhami@mdc-berlin.de> writes:
> * gnu/packages/bioconductor.scm (r-hdcytodata): New variable.
> ---
> gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++
> 1 file changed, 40 insertions(+)
>
> diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
> index d603bd42c1..1cf33501d6 100644
> --- a/gnu/packages/bioconductor.scm
> +++ b/gnu/packages/bioconductor.scm
> @@ -560,6 +560,46 @@ (define-public r-hdo-db
>
> https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology}.";)
> (license license:artistic2.0)))
Looks like this was committed as
f7682c247504d252cf86b274ffe7b8f62670b497.
Thanks,
Chris
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