From 248f766f7d8cf616e23f741965cfa5210589be9e Mon Sep 17 00:00:00 2001
From: Robert Kalescky <rkalescky@smu.edu>
Date: Fri, 10 Feb 2023 10:26:58 -0600
Subject: [PATCH 1/2] Biostats: Update to R packages.

---
 biostats_mcgee/Dockerfile         | 8 ++++----
 biostats_mcgee/install_packages.R | 7 ++++++-
 2 files changed, 10 insertions(+), 5 deletions(-)

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/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(

From c9b63da85f7d3fc8f8e5316e7dc722063cc9dfc3 Mon Sep 17 00:00:00 2001
From: Robert Kalescky <rkalescky@smu.edu>
Date: Fri, 10 Feb 2023 10:49:47 -0600
Subject: [PATCH 2/2] =?UTF-8?q?Still=20need=20to=20rename=20image=E2=80=A6?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

docker2singularity changes the extension to .simg instead of .sif. The file is actually a .sif. See: https://github.com/apptainer/singularity/issues/5178
---
 biostats_mcgee/build_images.sh | 1 +
 1 file changed, 1 insertion(+)

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