From 9dbac0360c1d7ea306d42adbc66dc37e778c1320 Mon Sep 17 00:00:00 2001
From: James Abbott <j.abbott@dundee.ac.uk>
Date: Thu, 25 May 2023 18:43:10 +0100
Subject: [PATCH] Ensure consistency in behaviour between normal and
 singularity scripts

---
 run_colabfold.sh             | 6 ++++--
 run_colabfold_singularity.sh | 3 ++-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/run_colabfold.sh b/run_colabfold.sh
index c590482..6042cdf 100755
--- a/run_colabfold.sh
+++ b/run_colabfold.sh
@@ -49,8 +49,10 @@ fi
 
 echo "Hostname: $HOSTNAME"
 echo "GPU: $CUDA_VISIBLE_DEVICES"
-echo "Command line: 'colabfold_batch  ${colabfold_args_list[@]} ${input} colabfold_outputs"
+echo "Command line: colabfold_batch  ${colabfold_args_list[@]} ${input} ${input_dir}/colabfold_outputs"
+
+input_dir=$(dirname $input)
 
 TF_CPP_MIN_LOG_LEVEL=2
-colabfold_batch ${colabfold_args_list[@]} ${input} colabfold_outputs
+colabfold_batch ${colabfold_args_list[@]} ${input} ${input_dir}/colabfold_outputs
 
diff --git a/run_colabfold_singularity.sh b/run_colabfold_singularity.sh
index 2be190e..8c83da9 100755
--- a/run_colabfold_singularity.sh
+++ b/run_colabfold_singularity.sh
@@ -59,7 +59,8 @@ fasta_file=$(basename $input)
 
 echo "Hostname: $HOSTNAME"
 echo "GPU: $CUDA_VISIBLE_DEVICES"
-echo "Command line: colabfold_batch ${colabfold_args_list[@]} ${input} colabfold_outputs"
+# This is a bit of a lie, but is the effective command run taking bind mounts into account...
+echo "Command line: colabfold_batch ${colabfold_args_list[@]} ${input} ${input_dir}/colabfold_outputs"
 
 export TF_CPP_MIN_LOG_LEVEL=2
 singularity exec --nv -B ${input_dir}:/mnt ${image} \