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I send this only in the case if the reviewer wants to dig more and maybe he can solve the non deterministic build. --- gnu/packages/bioconductor.scm | 138 ++++++++++++++++++++++++++++++++++ 1 file changed, 138 insertions(+) base-commit: efa091f9f4e77068353dff24f0ccd2d0613c3f48 prerequisite-patch-id: 9e08f9ff2621a13d751e3d82c0837144b09494e4 prerequisite-patch-id: 4cfeb51eeb402b18b0d23c6782255a3bc1f1ff43 prerequisite-patch-id: cf4c417ccd15ef1f795ada39f3faee9f59bb3c36 prerequisite-patch-id: d79a8e82e46ec03cf54f25ec101a5b54592fdb1b prerequisite-patch-id: 81871608ddab1ba624de7432ad473e52221efc08 diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7de5750e09..15fad711af 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -33,6 +33,7 @@ (define-module (gnu packages bioconductor) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix gexp) #:use-module (guix git-download) #:use-module (guix build-system r) #:use-module (gnu packages) @@ -6533,6 +6534,80 @@ (define-public r-limma different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-maaslin2 + (package + (name "r-maaslin2") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Maaslin2" version)) + (sha256 + (base32 "0ncvsywn9f8766gjb8nxzg82p3w30g8pjs85sy8s0bz9ilanpy89")))) + (properties `((upstream-name . "Maaslin2"))) + (build-system r-build-system) + (arguments (list ;;#:tests? #f)) ;test suite is non-deterministic :( + #:phases + #~(modify-phases %standard-phases + ;; During the check there is needed for writable cache directory + ;; Fontconfig error: No writable cache directories + (add-before 'check 'set-cache + (lambda _ + (setenv "XDG_CACHE_HOME" "/tmp/xdg-cache"))) + ;; The check phase generates some log and pdf files. This cause that + ;; the build to be not reproducible + (add-after 'check 'make-reproducible + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (string-append (assoc-ref outputs "out") "/site-library/Maaslin2/"))) + (for-each delete-file-recursively + (list ;;(string-append out "Maaslin2-Ex.Rout") + ;;(string-append #$output "/Maaslin2-Ex.pdf") + ;;(string-append #$output "/Maaslin2-tests/testthat/output") + ;;(string-append #$output "/Maaslin2-tests/testthat/output2") + ;;(string-append #$output "Maaslin2-tests/testthat.Rout") + (string-append out "doc/demo_output/maaslin2.log") + (string-append out "doc/demo_output/figures") + ;;"doc/demo_output" + ))))) + ))) + (propagated-inputs + (list r-biglm + r-car + r-chemometrics + r-cplm + r-data-table + r-dplyr + r-edger + r-ggplot2 + r-glmmtmb + r-hash + r-lme4 + r-lmertest + r-logging + r-lpsymphony + r-mass + r-mumin + r-metagenomeseq + r-optparse + r-pbapply + r-pcapp + r-pheatmap + r-pscl + r-rmarkdown + r-robustbase + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "http://huttenhower.sph.harvard.edu/maaslin2") + (synopsis + "Multivariable association discovery in population-scale meta-omics studies") + (description + "MaAsLin2 is comprehensive R package for efficiently determining multivariable +association between clinical metadata and microbial meta'omic features. This +package relies on general linear models to accommodate most modern epidemiological +study designs, including cross-sectional and longitudinal, and offers a variety +of data exploration, normalization, and transformation methods.") + (license license:expat))) + (define-public r-made4 (package (name "r-made4") @@ -6760,6 +6835,69 @@ (define-public r-methylkit 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")))) + (properties `((upstream-name . "MMUPHin"))) + (build-system r-build-system) + (arguments + (list ;;#:tests? #f)) ;; non deterministic, also it requieres http access + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'adjusts-paths + (lambda* (#:key inputs outputs #:allow-other-keys) + (substitute* "inst/doc/MMUPHin.Rmd" + (("../man/figures") + (string-append #$output "/site-library/MMUPHin/help/figures"))) + ;;(substitute* "inst/doc/MMUPHin.R" + ;; (("library(ggplot2)") "library(ggplot2)\ngetwd()")) + )) + (add-after 'install 'add-files + (lambda* (#:key inputs outputs #:allow-other-keys) + (install-file "man/figures/structure_types.PNG" + (string-append #$output "/site-library/MMUPHin/help/figures")) + (install-file "vignettes/references.bib" + (string-append #$output "/site-library/MMUPHin/doc")))) + (add-before 'check 'set-cache + (lambda _ + (setenv "XDG_CACHE_HOME" "/tmp/xdg-cache"))) + ))) + (inputs (list glpk + ; ;;pandoc + ; ;;r-rmarkdown + )) + (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")