Merge pull request #76 from kjsanger/devel

Fix singularity-wrapper script

singularity/scripts/singularity-wrapper

@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 #
 # Copyright (C) 2023 Genome Research Ltd. All rights reserved.
 #
@@ -17,7 +17,7 @@
 #
 # Author: Keith James <kdj@sanger.ac.uk>
 
-# set -euo pipefail ## FIXME: bashism
+set -euo pipefail
 
 usage() {
     cat 1>&2 << EOF
@@ -36,7 +36,7 @@ Usage: $0
     [-e]
     [-h]
     [-i <Docker image name>]
-    [-m <manifest path>]
+    [-m <JSON manifest path>]
     [-p <wrapper install prefix>]
     [-r <Docker registry name>]
     [-s]
@@ -73,7 +73,7 @@ EOF
 
 # Print an application manifest
 print_manifest() {
-    cat "$MANIFEST_PATH"
+    jq . "$MANIFEST_PATH"
 }
 
 # Write a bash script wrapping an application in a Docker container
@@ -113,9 +113,9 @@ install_wrappers() {
     install -d "$dir"
     cp "/usr/local/bin/$singularity_wrap_impl" "$PREFIX/bin"
 
-    while IFS= read -r exe; do
+    for exe in "${wrappers[@]}" ; do
         write_wrapper "$dir" "$exe"
-    done < "$MANIFEST_PATH"
+    done
 }
 
 DOCKER_REGISTRY=${DOCKER_REGISTRY:-ghcr.io}
@@ -124,7 +124,7 @@ DOCKER_IMAGE=${DOCKER_IMAGE:-""}
 DOCKER_TAG=${DOCKER_TAG:-latest}
 
 PREFIX=${PREFIX:-/opt/wtsi-npg}
-MANIFEST_PATH=${MANIFEST_PATH:-"$PREFIX/etc/manifest.txt"}
+MANIFEST_PATH=${MANIFEST_PATH:-"$PREFIX/etc/manifest.json"}
 
 singularity_wrap_impl="singularity-run-docker"
 
@@ -171,11 +171,18 @@ done
 
 shift $((OPTIND -1))
 
+declare -a wrappers
 if [ ! -e "$MANIFEST_PATH" ] ; then
     echo -e "\nERROR:\n  The manifest of executables at '$MANIFEST_PATH' does not exist"
     exit 4
 fi
 
+
+
+
+
+wrappers=($(jq -j '.executable[] + " "' "$MANIFEST_PATH"))
+
 operation="$@"
 if [ -z "$operation" ] ; then
     usage