Commit 5cb4f8c1 authored by josh's avatar josh
Browse files

Merge branch 'staging'

parents 4de76633 1fac5c53
Pipeline #204476 passed with stage
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......@@ -185,6 +185,8 @@ RUN apt-get update && \
librdp-taxonomy-tree-java \
clustalw \
fastqc \
ncbi-blast+ \
mothur \
libgsl-dev gsl-bin # for topicmodels
# sra-toolkit ipython python3-igraph \
......@@ -198,13 +200,15 @@ 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')" && \
Rscript -e "devtools::install_github('yiluheihei/microbiomeMarker')" && \
# Trans-ABySS
RUN mkdir -p $MANUAL_BIN $MANUAL_SHARE ; \
......
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