https://github.com/fhcrc/deenurp
Tip revision: 8f476da4bb0b417caf0afbbcb27522846820d683 authored by crosenth on 29 May 2019, 20:53:55 UTC
fixing timeout error
fixing timeout error
Tip revision: 8f476da
singularity-build-local.sh
#!/bin/bash
# build from a local docker image
set -e
if [[ -z $1 ]]; then
echo "usage: ./build.sh TAG [<outdir>]"
echo
echo "choose from one of the following tags:"
echo
docker image list deenurp
exit 1
fi
outdir=$(readlink -f ${2-.})
version=$1
docker_image=deenurp:$1
docker_name=$(echo $docker_image | tr : _)_$RANDOM
img=$(readlink -f $outdir/deenurp-${version}.img)
if [[ -f $img ]]; then
echo "$img already exists"
exit 1
fi
# supposedly how it should be done for singularity 2.4
# must disable user namespaces with --userns=host to use --privileged
docker run \
-v /var/run/docker.sock:/var/run/docker.sock \
-v $outdir:/output \
--privileged --userns=host -t --rm \
docker2singularity:2.3 \
$docker_image
# singularity create --size 2300 $img
# docker run --name $docker_name $docker_image /bin/true
# docker export $docker_name | sudo singularity import $img
# docker rm $docker_name
# sudo singularity exec --writable $img mkdir -p /fh /app /mnt