update

Dockerfile

@@ -1,4 +1,4 @@
-FROM r-base:4.3.1
+FROM r-base:4.3.2
 
 LABEL \
     author="Shixiang Wang" \
@@ -10,19 +10,17 @@ LABEL \
     org.label-schema.vendor="XSLiu Lab Project"
 
 ## Install system dependencies
-RUN apt update -y && apt install -y libcurl4-openssl-dev libxml2-dev libssl-dev cmake build-essential &&  \
-    apt autoremove -y && apt clean -y && apt purge -y && rm -rf /tmp/* /var/tmp/*
+RUN apt update -y && apt install -y libcurl4-openssl-dev libxml2-dev libssl-dev cmake build-essential
 ## Install R packages which are easy to install
-RUN R -e "install.packages('BiocManager', repos = 'https://cloud.r-project.org')" && \
-    R -e "BiocManager::install(c('remotes', 'data.table', 'dplyr', 'purrr', 'tidyr', 'furrr', 'Rcpp', 'cowplot', 'NMF', 'ggpubr', 'cli', 'reticulate', 'roxygen2'))"
 ## Install reference genome packages which are big
-RUN R -e "BiocManager::install('BSgenome')" && \
+## Install sigminer
+RUN R -e "install.packages('BiocManager', repos = 'https://cloud.r-project.org')" && \
+    R -e "BiocManager::install(c('remotes', 'data.table', 'dplyr', 'purrr', 'tidyr', 'furrr', 'Rcpp', 'cowplot', 'NMF', 'ggpubr', 'cli', 'reticulate', 'roxygen2'))" && \
+    R -e "BiocManager::install('BSgenome')" && \
     R -e "BiocManager::install('BSgenome.Hsapiens.UCSC.hg19')" && \
     R -e "BiocManager::install('BSgenome.Hsapiens.UCSC.hg38')" && \
-    R -e "BiocManager::install('BSgenome.Mmusculus.UCSC.mm10')"
-## Install sigminer
-RUN R -e "BiocManager::install('ShixiangWang/[email protected]', dependencies = TRUE)" && \
-    rm -rf /tmp/* /var/tmp/* && \
+    R -e "BiocManager::install('BSgenome.Mmusculus.UCSC.mm10')" && \
+    R -e "BiocManager::install('ShixiangWang/[email protected]', dependencies = TRUE)" && \
     R -e "library('sigminer'); load(system.file('extdata', 'toy_copynumber_tally_W.RData', package = 'sigminer', mustWork = TRUE)); mat = cn_tally_W[['nmf_matrix']]; print(mat);"
 ## Copy sigflow program and run test
 ## It is strange that the docopt cannot be installed to the first location
@@ -33,7 +31,8 @@ RUN chmod -R a+w /usr/local/lib/R/site-library && \
     R --vanilla -f /opt/pkg_check.R && \
     R -e "install.packages('docopt', lib = .libPaths()[2])" && \
     chmod u+x /opt/sigflow.R && ln -s /opt/sigflow.R /usr/bin/sigflow && \
-    cd /opt/test && chmod u+x test.sh && ./test.sh && rm -rf test_results && cd /root
+    cd /opt/test && chmod u+x test.sh && ./test.sh && rm -rf test_results && cd /root && \
+    apt autoremove -y && apt clean -y && apt purge -y && rm -rf /tmp/* /var/tmp/*
 WORKDIR /root
 ## Deploy
 ## When ENTRYPOINT is used, the docker can be only run as a command