Commit 45d835fe authored by Josh's avatar Josh
Browse files

Added Daniel's phylogeetic tree packages

parent 4fb9b59d
......@@ -194,13 +194,13 @@ RUN Rscript -e "install.packages(pkgs = c('tidyverse','caTools','rprojroot','rma
# Add microbiome specific R and bioconductor packages
RUN Rscript -e "install.packages(pkgs = c('fs','phangorn','ips','unvotes','DT','sandwich','TH.data', 'here', 'sf', 'spdep', 'agricolae'), \
RUN Rscript -e "install.packages(pkgs = c('fs','ips','unvotes','DT','sandwich','TH.data', 'here', 'sf', 'spdep', 'agricolae'), \
repos='https://cran.revolutionanalytics.com/', \
dependencies=TRUE, \
clean = TRUE)"
RUN Rscript -e "if (!requireNamespace('BiocManager')){install.packages('BiocManager')}; \
BiocManager::install(c('dada2','ShortRead','phyloseq','msa','DESeq2','metagenomeSeq','DECIPHER','ALDEx2'))"
BiocManager::install(c('dada2','ShortRead','phyloseq','msa','DESeq2','metagenomeSeq','ALDEx2'))"
# 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"
......@@ -309,6 +309,34 @@ RUN mkdir -p $MANUAL_BIN download && \
mv download/raxml-ng $MANUAL_BIN && \
rm -rf 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')"
#SEPP for greengenes
RUN cd /opt && \
wget https://raw.github.com/smirarab/sepp-refs/master/gg/sepp-package.tar.bz && \
tar -xjf sepp-package.tar.bz && \
cd /opt/sepp-package/sepp && \
python3 setup.py config -c && \
chmod -R 555 /opt/sepp-package && \
rm /opt/sepp-package.tar.bz
#GAPPA
RUN cd /opt && \
git clone --recursive https://github.com/lczech/gappa.git /opt/gappa && \
cd /opt/gappa && \
make
#EPA-NG
RUN cd /opt && \
git clone --recursive https://github.com/Pbdas/epa-ng /opt/epa-ng && \
cd /opt/epa-ng && \
make
# UNDER CONSTRUCTION: Nerd Work Zone <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
RUN apt-get clean && \
......
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