Add ability to get usage information from colabfold_batch

README.md

@@ -27,13 +27,13 @@ All necessary components are already available on the cluster.
 1. Obtain a copy of this repository either using git i.e.  
 `git clone git://github.com/bartongroup/JCA_colabfold_batch.git`  
 or by downloading a release tarball from the link on the right under 'Releases'. Copy this tarball onto the cluster filesystem and extract with  
-`tar zxvf v1.5.2-beta2.tar.gz`
+`tar zxvf v1.5.2-beta3.tar.gz`
 
 2. Change into the directory which is created by step 1 - this will have the repository name if cloned from git, or the version number if obtained from a Release tarball.
 a)  From a repository clone:  
 `cd Colabfold_batch_installer`  
 b) From a release tarball:  
-`cd Colabfold_batch_installer-1.5.2-beta2`
+`cd Colabfold_batch_installer-1.5.2-beta3`
 
 3. Run the setup script:  
 `./setup.sh`  
@@ -43,11 +43,13 @@ This will create a new conda environment named `colabfold_batch` based upon the
 
 ### Singularity
 
-Usage: run_colabfold_singularity.sh -i /path/to/fasta/file [-c 'colabfold arguments']
+Usage: run_colabfold_singularity.sh -i /path/to/fasta/file [-c 'colabfold arguments'] [-h] [-u]
 
 The `run_colabfold_singularity.sh` script can be submitted directly to GridEngine, and requires at a minimun the path to an input fasta file. Any specific colabfold arguments can be provided using the `-c` argument. Log files will be written to a 'colabfold_logs' directory in the submission directory, while outputs will be written to a `colabfold_outputs` directory within the directory containing the submitted fasta file. 
 
-i.e. `qsub /path/to/run_colabfold.sh -i test/cadh5_arath.fa -c "--num-recycle 5 --amber --num-relax 5"`  
+i.e. `qsub /path/to/run_colabfold_singularity.sh -i test/cadh5_arath.fa -c "--num-recycle 5 --amber --num-relax 5"`  
+
+Full colabfold usage information can be found by running `run_colabfold_singularity.sh -u`
 
 ### Full Installation
 
@@ -73,6 +75,8 @@ Resulting job logs will be written into a subdirectory of the submission directo
 
 **N.B. There are known issues with alphafold in relaxing models using Amber on GPUs - if this fails, omit the `--use-gpu-relax` argument and run amber only on CPUs - This part of the process on CPUs doesn't seem overly slow**
 
+Full colabfold usage information can be found by running `run_colabfold.sh -u`
+
 ## Limitations
 
 At present we do not have an in-house MMSeq2 server, so queries are directed to the default public server, which has limited capacity. Also bear in mind that use of a public resource would expose data externally which may not be appropriate.

run_colabfold.sh

@@ -10,19 +10,31 @@
 set -e
 
 usage() {
-	echo "$0 -i /path/to/fasta/file [-c 'colabfold arguments']"
+	echo "Usage: $0 -i /path/to/fasta/file [-c 'colabfold arguments'] [-h] [-u]"
+	echo
+	echo "Note that colabfold arguments passed via '-c' must be surrounded with quotes to ensure they are all passed to colabfold"
+	echo
+	echo "run $0 -u for colabfold_batch help"
+	echo
 	exit 1
 }
 
+colabfold_usage() {
+	colabfold_batch -h
+	exit 1
+}
 
-while getopts "i:c:h" opt; do
+while getopts "i:c:uh" opt; do
 	case $opt in
 		i)
 			input=$OPTARG
 			;;
 		c)
 			colabfold_args=$OPTARG
 			;;
+		u)
+			colabfold_usage
+			;;
 		h)
 			usage
 			;;
@@ -40,7 +52,6 @@ for arg in "${colabfold_args_list[@]}"; do
 		echo "Should this occur, rerun without --use-gpu-relax"
 		echo
 	fi
-
 done
 
 if [[ -z "$input" ]]; then

run_colabfold_singularity.sh

@@ -12,18 +12,32 @@ set -e
 image='/cluster/gjb_lab/cdr/colabfold/colabfold_batch.1.5.2.sif'
 
 usage() {
-	echo "$0 -i /path/to/fasta/file [-c 'colabfold arguments']"
+	echo "Usage: $0 -i /path/to/fasta/file [-c 'colabfold arguments'] [-h] [-u]"
+	echo
+	echo "Note that colabfold arguments passed via '-c' must be surrounded with quotes to ensure they are all passed to colabfold"
+	echo
+	echo "run $0 -u for colabfold_batch help"
+	echo
 	exit 1
 }
 
-while getopts "i:c:h" opt; do
+colabfold_usage() {
+	export TINI_SUBREAPER=1
+	singularity run ${image} colabfold_batch -h
+	exit 1
+}
+
+while getopts "i:c:uh" opt; do
 	case $opt in
 		i)
 			input=$OPTARG
 			;;
 		c)
 			colabfold_args=$OPTARG
 			;;
+		u)
+			colabfold_usage
+			;;
 		h)
 			usage
 			;;
@@ -36,7 +50,7 @@ read -a colabfold_args_list <<< "$colabfold_args"
 
 for arg in "${colabfold_args_list[@]}"; do
 	if [[ "$arg" == "--use-gpu-relax" ]]; then
-	 	echo
+		echo
 		echo "WARNING: Running amber relaxation on GPUs is unreliable and may fail."
 		echo "Should this occur, rerun without --use-gpu-relax"
 		echo
@@ -63,5 +77,6 @@ echo "GPU: $CUDA_VISIBLE_DEVICES"
 echo "Command line: colabfold_batch ${colabfold_args_list[@]} ${input} ${input_dir}/colabfold_outputs"
 
 export TF_CPP_MIN_LOG_LEVEL=2
+export TINI_SUBREAPER=1
 singularity exec --nv -B ${input_dir}:/mnt ${image} \
-	colabfold_batch ${colabfold_args_list[@]} /mnt/${fasta_file} /mnt/colabfold_output
+	colabfold_batch ${colabfold_args_list[@]} /mnt/${fasta_file} /mnt/colabfold_output