organisation fixes

03-prs.sh

@@ -139,5 +139,5 @@ done
 
 echo "Successfully generated correlation matrices for each phenotype!"
 echo "Generating PRS-phenotype associations for each subset"
-Rscript resources/phenotypes/score.r ${phenotype_processed_dir}/phenolist ${genotype_processed_dir}/scratch/tophits ${results_dir}/04
+Rscript resources/phenotypes/score.r ${phenotype_processed_dir}/phenolist ${genotype_processed_dir}/scratch/tophits ${results_dir}/03
 echo "Successfully generated scores!"

utils/check.sh

@@ -2,9 +2,42 @@
 
 source config.env
 
+
+echo "Checking R packages..."
 Rscript -e "renv::status()"
 
-./bin/plink2 --version
-./bin/flashpca --version
-./bin/gcta-1.94.1
-./bin/king
+tf=$(mktemp)
+
+echo "Checking plink..."
+if ./bin/plink2 --version > $tf 2>&1; then
+    echo "All good!"
+else
+    cat $tf
+fi
+
+echo "Checking flashpca..."
+if ./bin/flashpca --version > $tf 2>&1; then
+    echo "All good!"
+else
+    cat $tf
+fi
+
+echo "Checking gcta..."
+
+./bin/gcta-1.94.1 > $tf 2>&1
+if cat $tf | grep -q "Genome"; then
+    echo "All good!"
+else
+    cat $tf
+fi
+
+echo "Checking gcta..."
+
+./bin/king > $tf 2>&1
+if cat $tf | grep -q "KING"; then
+    echo "All good!"
+else
+    cat $tf
+fi
+
+

utils/run_apptainer.sh

@@ -2,24 +2,25 @@
 
 source config.env
 
-apptainer pull -F docker://MRCIEU/lifecourse-gwas:latest
+# apptainer pull -F docker://mrcieu/lifecourse-gwas:latest
 
 # Run without pwd binding
 
-d=${PWD}
-echo $d
-td=$(mktemp -d)
-cd $td
+# d=${PWD}
+# echo $d
+# td=$(mktemp -d)
+# cd $td
 
 apptainer run \
-    --bind "${d}/config.env:/project/config.env" \
+    --containall \
+    --bind "${PWD}/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 \
+    ${PWD}/lifecourse-gwas_latest.sif \
     "$@"
 
-cd $d
+# cd $d