ssh_wrapper.sh

#!/bin/bash
# is /usr/bin/ssh inside a container
# 05/11/2016 Antoine Schonewille
# 05/18/2016 Revision -A
# 01/06/2016 stefan.kombrink@uni-ulm.de - adjustments for bwForCluster Ulm (JUSTUS)
# 23/11/2016 stefan.kombrink@uni-ulm.de - adjustments for singularity

# works with openssh supplied in RHEL 6 and 7

_LOCALHOST='localhost'
_LOCALIP='127.0.0'
_HOSTNAME=`hostname --short`
_HAS_PARAMS="bcDeFIiLlmOopRSWw"

while (( "$#" )); do
        _ONE=`echo $@|cut -f1 -d' '`
        _TWO=`echo $@|cut -f2 -d' '`
        # easy. if a word starts with an hyphen it's an option and it might come with a parameter
        if [ "`echo $_ONE | cut -b1`" == "-" ]; then
                _PARAM=$_PARAM' '$_ONE
                _PREV='option'
                if [ "$(echo $_HAS_PARAMS | grep `echo $_ONE | cut -b2`)" ] && [ "`echo $_ONE | cut -b3`" == "" ]; then
                        _PARAM=$_PARAM' '$_TWO
                        shift
                fi
        else
                # if the current word does not have a hyphen (no option) then we have two possibilities
                #  a: previous word wasn't an option (hyphen) 
                #  b: or the second word doesn't have a hyphen (part of command)
                # both cases then assume that the host must be the first word 
                if [ "$_PREV" != "option" ] || [ "`echo $_TWO | cut -b1`" != "-" ]; then
                        _HOST=$_ONE
                        shift
                        _COMMAND=$@
                        break
                else
                        _PARAM=$_PARAM' '$_ONE
                        _PREV=''
                fi
        fi
        shift
done

_COMMAND=`echo $_COMMAND | tr '"' "'"`

# with no params start an singularity container remotely with a pseudy TTY
if [ "$_COMMAND" == "" ]; then
    _PARAM="-t $_PARAM"
    _COMMAND="/bin/bash"
else
    _COMMAND='/bin/bash -c "'$_COMMAND'"'
fi

echo "====="
echo /usr/bin/ssh_orig $_PARAM $_HOST \$\(which singularity\) exec -B /etc/ssh $SINGULARITY_IMAGE $_COMMAND
/usr/bin/ssh_orig $_PARAM $_HOST \$\(which singularity\) exec -B /etc/ssh $SINGULARITY_IMAGE $_COMMAND

exit $?