diff options
| -rw-r--r-- | gnu/packages/bioconductor.scm | 69 |
1 files changed, 69 insertions, 0 deletions
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") |