add podman wrapper

bakta-podman.sh

@@ -0,0 +1,73 @@
+#!/bin/bash
+set -eo pipefail
+
+# ToDo: set final namespace
+IMAGE=quay.io/biocontainers/bakta:1.8.2--pyhdfd78af_0
+DEFAULT_DBPATH=$BAKTA_DB
+
+args=( "$@" )
+argcount=${#args[@]}
+
+# handle help parameter separately
+if [[ $argcount -eq 0 || " ${args[@]} " =~ " --help " || " ${args[@]} " =~ " -h " ]]; then
+    podman run -it --rm $IMAGE bakta --help
+    exit $?
+fi
+
+# run bakta podman
+# decisions:
+# all parameters are passed through, except genome, db and output
+# they are replaced with their absolute paths and are mounted to
+# the container
+
+CWD=$(realpath .)
+DB=
+OUTPUT=
+GENOME=$(realpath ${args[$argcount-1]})
+args[$((argcount-1))]=$GENOME
+
+for i in `seq 0 $((argcount-1))`; do
+    VAL=${args[i]}
+    j=$((i+1))
+    if [[ "$VAL" == "--db" || "$VAL" == "-d" ]]; then
+        DB=${args[j]}
+        DB=$(realpath $DB)
+        args[j]=$DB
+    fi
+    if [[ "$VAL" == "--output" || "$VAL" == "-o" ]]; then
+        OUTPUT=${args[j]}
+        OUTPUT=$(realpath $OUTPUT)
+        args[j]=$OUTPUT
+    fi
+done;
+
+if [[ -z "$DB" ]]; then
+    DB=$DEFAULT_DBPATH
+fi
+if [[ -z "$OUTPUT" ]]; then
+    OUTPUT=$PWD
+fi
+if [[ ! -d "$OUTPUT" ]]; then
+    mkdir -p "$OUTPUT"
+fi
+
+echo "******************************"
+echo "* bakta podman wrapper       *"
+echo "******************************"
+echo "*       # Arguments: " $argcount
+echo "* Database location: " $DB
+echo "*   Genome location: " $GENOME
+echo "*  Output location : " $OUTPUT
+echo "******************************"
+CMD=$(cat <<-END
+    podman run -it --rm \
+    -v $DB:$DB:ro \
+    -v $OUTPUT:$OUTPUT:rw \
+    -v $GENOME:$GENOME:ro \
+    --workdir $CWD \
+    $IMAGE bakta --force ${args[@]}
+END
+)
+echo "* Commandline: " $CMD
+echo "******************************"
+$CMD