# -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4

PortSystem          1.0
PortGroup           R 1.0

R.setup             bioconductor tgirke systemPipeR 2.10.0
revision            0
categories-append   bioconductor
maintainers         nomaintainer
license             Artistic-2
description         NGS workflow and report generation environment
long_description    {*}${description}
homepage            https://systempipe.org
checksums           rmd160  122d5be0dadad2c061b2d8479e2306de82076b6d \
                    sha256  dde61514c472f019a4e8a5bc46b09c4ec7daac41ec994ddf2fc443583c66bd8f \
                    size    7419683
supported_archs     noarch

depends_lib-append  port:R-BiocGenerics \
                    port:R-Biostrings \
                    port:R-crayon \
                    port:R-GenomicRanges \
                    port:R-ggplot2 \
                    port:R-htmlwidgets \
                    port:R-magrittr \
                    port:R-Rsamtools \
                    port:R-S4Vectors \
                    port:R-ShortRead \
                    port:R-stringr \
                    port:R-SummarizedExperiment \
                    port:R-yaml

patchfiles-append   patch-no-GO.db.diff

depends_test-append port:R-annotate \
                    port:R-AnnotationDbi \
                    port:R-batchtools \
                    port:R-BiocStyle \
                    port:R-DESeq2 \
                    port:R-dplyr \
                    port:R-DT \
                    port:R-edgeR \
                    port:R-GenomeInfoDb \
                    port:R-GenomicAlignments \
                    port:R-GenomicFeatures \
                    port:R-IRanges \
                    port:R-kableExtra \
                    port:R-knitr \
                    port:R-limma \
                    port:R-rjson \
                    port:R-rmarkdown \
                    port:R-rtracklayer \
                    port:R-testthat \
                    port:R-systemPipeRdata \
                    port:R-VariantAnnotation

test.run            yes
