wrapper for containers

.dockerignore

@@ -0,0 +1,4 @@
+renv/library
+renv/staging
+.git
+config.env

Dockerfile

@@ -43,3 +43,4 @@ RUN R -e 'options( \
     install.packages("renv", dependencies = TRUE); \
     renv::restore()'
 
+COPY . .

check.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+source config.env
+
+Rscript -e "renv::status()"
+
+./bin/plink2 --version
+./bin/flashpca --version
+./bin/gcta-1.94.1
+./bin/king

run_apptainer.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+
+source config.env
+
+apptainer pull -F docker://MRCIEU/lifecourse-gwas:latest
+
+# Run without pwd binding
+
+d=${PWD}
+echo $d
+td=$(mktemp -d)
+cd $td
+
+apptainer run \
+    --bind "${d}/config.env:/project/config.env" \
+    --bind "${phenotype_input_dir}:${phenotype_input_dir}" \
+    --bind "${phenotype_processed_dir}:${phenotype_processed_dir}" \
+    --bind "${genotype_input_dir}:${genotype_input_dir}" \
+    --bind "${genotype_processed_dir}:${genotype_processed_dir}" \
+    --bind "${results_dir}:${results_dir}" \
+    --cwd /project \
+    ${d}/lifecourse-gwas_latest.sif \
+    "$@"
+
+cd $d

run_docker.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+set -e
+
+source config.env
+
+# docker build -t mrcieu/lifecourse-gwas:latest .
+# docker pull mrcieu/lifecourse-gwas:latest
+
+docker run \
+    -v "${PWD}/config.env:/project/config.env:ro" \
+    -v ${phenotype_input_dir}:${phenotype_input_dir} \
+    -v ${phenotype_processed_dir}:${phenotype_processed_dir} \
+    -v ${genotype_input_dir}:${genotype_input_dir} \
+    -v ${genotype_processed_dir}:${genotype_processed_dir} \
+    -v ${results_dir}:${results_dir} \
+    MRCIEU/lifecourse-gwas:latest \
+    "$@"