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branch master updated: gnu: Add r-mmuphin.
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guix-commits |
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branch master updated: gnu: Add r-mmuphin. |
Date: |
Thu, 02 Mar 2023 14:11:34 -0500 |
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rekado pushed a commit to branch master
in repository guix.
The following commit(s) were added to refs/heads/master by this push:
new 5dae9d2683 gnu: Add r-mmuphin.
5dae9d2683 is described below
commit 5dae9d26831b6d092a80a123a2fc064326d4a8ba
Author: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
AuthorDate: Wed Mar 1 08:16:27 2023 +0100
gnu: Add r-mmuphin.
* gnu/packages/bioconductor.scm (r-mmuphin): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
---
gnu/packages/bioconductor.scm | 69 +++++++++++++++++++++++++++++++++++++++++++
1 file changed, 69 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2bfca85bbc..22be8d3772 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6880,6 +6880,75 @@ resolution 5hmC data from experimental protocols such as
oxBS-Seq and
TAB-Seq.")
(license license:artistic2.0)))
+(define-public r-mmuphin
+ (package
+ (name "r-mmuphin")
+ (version "1.12.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MMUPHin" version))
+ (sha256
+ (base32 "0vpap3avmrjy187s3dva6f008al6d935kpdf816xzl5gxl7zvf62"))
+ ;; Delete generated files.
+ (snippet
+ '(for-each delete-file
+ '("inst/doc/MMUPHin.R"
+ "inst/doc/MMUPHin.html")))))
+ (properties `((upstream-name . "MMUPHin")))
+ (build-system r-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'fix-includes
+ (lambda _
+ (substitute* "inst/doc/MMUPHin.Rmd"
+ (("\\.\\./man/figures")
+ (string-append (getcwd) "/man/figures"))
+ (("bibliography: references.bib")
+ (string-append "bibliography: "
+ (getcwd) "/vignettes/references.bib")))))
+ ;; Maaslin2 generates log files with timestamps. We don't need to
+ ;; keep them. The generated PDF files also contain timestamps, so
+ ;; we replace them with arbitrary fixed timestamps.
+ (add-after 'check 'make-reproducible
+ (lambda _
+ (for-each delete-file
+ (find-files #$output "maaslin2.log"))
+ (with-fluids ((%default-port-encoding "ISO-8859-1"))
+ (substitute* (find-files #$output "\\.pdf$")
+ (("/CreationDate \\(D:.*\\)")
+ "/CreationDate (D:20230301143558)")
+ (("/ModDate \\(D:.*\\)")
+ "/ModDate (D:20230301143558)"))))))))
+ ;; The DESCRIPTION file says that glpk is needed, but this package does
+ ;; not seem to reference the library directly.
+ (propagated-inputs
+ (list r-cowplot
+ r-biocstyle
+ r-dplyr
+ r-fpc
+ r-ggplot2
+ r-igraph
+ r-maaslin2
+ r-metafor
+ r-stringr
+ r-tidyr))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/MMUPHin")
+ (synopsis "Meta-analysis with uniform pipeline for heterogeneity in
microbiome")
+ (description
+ "MMUPHin is an R package for meta-analysis tasks of microbiome cohorts.
+It has function interfaces for:
+@itemize
+@item covariate-controlled batch- and cohort effect adjustment;
+@item meta-analysis differential abundance testing;
+@item meta-analysis unsupervised discrete structure (clustering) discovery;
+@item meta-analysis unsupervised continuous structure discovery.
+@end itemize")
+ (license license:expat)))
+
(define-public r-motifrg
(package
(name "r-motifrg")
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