Commit 9cf5ee30 authored by josh's avatar josh
Browse files

Install BLAST and R blast packages

parent 3c9b10f3
Pipeline #201519 passed with stages
in 141 minutes and 40 seconds
......@@ -185,6 +185,7 @@ RUN apt-get update && \
librdp-taxonomy-tree-java \
clustalw \
fastqc \
ncbi-blast+ \
libgsl-dev gsl-bin # for topicmodels
# sra-toolkit ipython python3-igraph \
......@@ -198,13 +199,14 @@ 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','ips','unvotes','DT','sandwich','TH.data', 'here', 'sf', 'spdep', 'agricolae','topicmodels','robCompositions'), \
RUN Rscript -e "install.packages(pkgs = c('fs','ips','unvotes','DT','sandwich','TH.data', 'here', 'sf', 'spdep', 'agricolae','topicmodels','robCompositions','rentrez'), \
repos=${CRAN_REPO}, \
dependencies=TRUE, \
clean = TRUE)"
RUN Rscript -e "if (!requireNamespace('BiocManager')){install.packages('BiocManager')}; \
BiocManager::install(c('dada2','ShortRead','phyloseq','msa','DESeq2','metagenomeSeq','ALDEx2','decontam','ANCOMBC','lefser'),version=$BIOCONDUCTOR_VERSION)"
BiocManager::install(c('dada2','ShortRead','phyloseq','msa','DESeq2','metagenomeSeq','ALDEx2','decontam','ANCOMBC','lefser', 'annotate','Biostrings'),version=$BIOCONDUCTOR_VERSION)" && \
Rscript -e "devtools::install_github('mhahsler/rBLAST',version=$BIOCONDUCTOR_VERSION)"
# Trans-ABySS
RUN mkdir -p $MANUAL_BIN $MANUAL_SHARE ; \
......
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