Commit 126663ef authored by josh's avatar josh
Browse files

Use bioconductor version 3.12 for everything

some bioconductor packages were pinnned to bioconductor 3.10, which is incompatible with R 4.0.X
parent 5423c272
Pipeline #194660 passed with stages
in 144 minutes and 18 seconds
......@@ -3,3 +3,5 @@
.RData
.Ruserdata
*.Rproj
build_output_*.txt
docker_build_output_*.txt
......@@ -7,6 +7,7 @@ MAINTAINER Mark McCahill "mark.mccahill@duke.edu"
ENV DEBIAN_FRONTEND noninteractive
ENV R_VERSION="4.0.4"
ENV BIOCONDUCTOR_VERSION="3.12"
ENV RSTUDIO_VERSION="1.2.5042"
ENV CRAN_REPO="'https://mran.revolutionanalytics.com/snapshot/2021-02-16'"
......@@ -202,7 +203,7 @@ 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','lefser'))"
BiocManager::install(c('dada2','ShortRead','phyloseq','msa','DESeq2','metagenomeSeq','ALDEx2','decontam','ANCOMBC','lefser'),version=$BIOCONDUCTOR_VERSION)"
# Trans-ABySS
RUN mkdir -p $MANUAL_BIN $MANUAL_SHARE ; \
......@@ -299,8 +300,8 @@ RUN mkdir -p $MANUAL_BIN download && \
# Daniel's packages for phylogenetic trees
#-----------------------------------------
RUN Rscript -e "install.packages(pkg='phangorn',repos='http://archive.linux.duke.edu/cran/',INSTALL_opts = c('--no-docs', '--no-help'))" && \
Rscript -e "BiocManager::install(c('philr','DECIPHER','ggtree'),version='3.10')" && \
Rscript -e "devtools::install_github('reptalex/phylofactor',version='3.10')"
Rscript -e "BiocManager::install(c('philr','DECIPHER','ggtree'),version=$BIOCONDUCTOR_VERSION)" && \
Rscript -e "devtools::install_github('reptalex/phylofactor',version=$BIOCONDUCTOR_VERSION)"
#SEPP for greengenes
RUN apt-get update && \
......@@ -388,7 +389,9 @@ EXPOSE 8787
CMD ["/usr/bin/supervisord"]
#----------------------------------------
# Not working yet:
# TODO
#----------------------------------------
## Not working yet:
#----------------------------------------
# lefser
# ANCOMBC
......@@ -400,3 +403,6 @@ CMD ["/usr/bin/supervisord"]
# shogun_bt2_lca
# shogun_utree_db
# shogun_utree_lca
#----------------------------------------
## Add version to all Bioconductor calls: BiocManager
#----------------------------------------
\ No newline at end of file
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