Commit 76889c79 authored by josh's avatar josh
Browse files

try adding lefseR (from bioconductor)

parent 902c2dc0
Pipeline #192342 passed with stages
in 68 minutes and 23 seconds
......@@ -201,7 +201,7 @@ RUN Rscript -e "install.packages(pkgs = c('fs','ips','unvotes','DT','sandwich','
clean = TRUE)"
RUN Rscript -e "if (!requireNamespace('BiocManager')){install.packages('BiocManager')}; \
BiocManager::install(c('dada2','ShortRead','phyloseq','msa','DESeq2','metagenomeSeq','ALDEx2','decontam','ANCOMBC'))"
BiocManager::install(c('dada2','ShortRead','phyloseq','msa','DESeq2','metagenomeSeq','ALDEx2','decontam','ANCOMBC','lefser'))"
# need to install older version of multcomp to avoid dependency on newer mvtnorm, which depends on newer R
# also needed to install multcomp dependencies: "sandwich","TH.data"
......
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