fixed container calls

MRCIEU · Jan 16, 2025 · 6a4b40e · 6a4b40e
1 parent 3cd60b2
commit 6a4b40e
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diff --git a/utils/run_apptainer.sh b/utils/run_apptainer.sh
@@ -11,9 +11,12 @@ source config.env
 # td=$(mktemp -d)
 # cd $td
 
+genotype_input_dir=$(head -n 1 geno_input.txt | awk '{ print $1 }' | xargs -I {} dirname {})
+
 apptainer run \
     --containall \
     --bind "${PWD}/config.env:/project/config.env" \
+    --bind "${PWD}/geno_input.txt:/project/geno_input.txt" \
     --bind "${phenotype_input_dir}:${phenotype_input_dir}" \
     --bind "${phenotype_processed_dir}:${phenotype_processed_dir}" \
     --bind "${genotype_input_dir}:${genotype_input_dir}" \

diff --git a/utils/run_docker.sh b/utils/run_docker.sh
@@ -7,8 +7,11 @@ source config.env
 # docker build -t mrcieu/lifecourse-gwas:latest .
 # docker pull mrcieu/lifecourse-gwas:latest
 
+genotype_input_dir=$(head -n 1 geno_input.txt | awk '{ print $1 }' | xargs -I {} dirname {})
+
 docker run \
     -v "${PWD}/config.env:/project/config.env:ro" \
+    -v "${PWD}/geno_input.txt:/project/geno_input.txt:ro" \
     -v ${phenotype_input_dir}:${phenotype_input_dir} \
     -v ${phenotype_processed_dir}:${phenotype_processed_dir} \
     -v ${genotype_input_dir}:${genotype_input_dir} \