Merge pull request #3 from SouthernMethodistUniversity/biostats_mcgee

Biostats mcgee
SouthernMethodistUniversity · Feb 10, 2023 · c8f44eb · c8f44eb
2 parents d8ad56a + c9b63da
commit c8f44eb
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Showing 3 changed files with 11 additions and 5 deletions.
diff --git 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
@@ -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
@@ -1,6 +1,11 @@
 cran = list(
   packages = c(
-    "BiocManager")
+    "BiocManager",
+    "ade4",
+    "vcfR",
+    "adegenet",
+    "reshape2",
+    "ggplot2")
 )
 
 bioc = list(