diff --git a/biostats_mcgee/Dockerfile b/biostats_mcgee/Dockerfile index 87470048..43ca4beb 100644 --- a/biostats_mcgee/Dockerfile +++ b/biostats_mcgee/Dockerfile @@ -69,10 +69,6 @@ RUN git clone --depth 1 --branch v1.3.3\ make -j install &&\ rm -rf /opt/RSEM -# Install R Packages -COPY install_packages.R / -RUN Rscript /install_packages.R - # GATK4 RUN git clone --depth 1 --branch 4.2.6.1\ https://github.com/broadinstitute/gatk.git /opt/gatk &&\ @@ -87,3 +83,7 @@ RUN git clone --depth 1 --branch v1.9.0\ cmake .. &&\ make install +# Install R Packages +COPY install_packages.R / +RUN Rscript /install_packages.R + diff --git a/biostats_mcgee/build_images.sh b/biostats_mcgee/build_images.sh index cda07043..e1085f05 100755 --- a/biostats_mcgee/build_images.sh +++ b/biostats_mcgee/build_images.sh @@ -28,6 +28,7 @@ docker build --no-cache --progress=plain\ docker run -v /var/run/docker.sock:/var/run/docker.sock\ -v $PWD:/output --privileged -t --rm singularityware/docker2singularity\ -n ${img} ${name}:${version} |& tee -a build.log +mv ${img%.sif}.simg ${img} # Change Singularity image permissions if [[ $(uname -s) == "Linux" ]]; then diff --git a/biostats_mcgee/install_packages.R b/biostats_mcgee/install_packages.R index 3df6cd2d..fd2d96e8 100644 --- a/biostats_mcgee/install_packages.R +++ b/biostats_mcgee/install_packages.R @@ -1,6 +1,11 @@ cran = list( packages = c( - "BiocManager") + "BiocManager", + "ade4", + "vcfR", + "adegenet", + "reshape2", + "ggplot2") ) bioc = list(