Homec4science
Diffusion eSCT pipeline interoperability (master) Browse

R2915/SIS/docker2singularity-master/docker2singularity.sh
2dda3e0d84camaster

Last Change
Raw File

docker2singularity.sh
View Options

#! /bin/bash
#
# docker2singularity.sh will convert a docker image into a singularity
# Must be run with sudo to use docker commands (eg aufs)
#
# NOTES:
# If the docker image uses both ENTRYPOINT and CMD the latter will be ignored
#
# KNOWN ISSUES:
# Currently ENTRYPOINTs and CMDs with commas in the arguments are not supported
#
# USAGE: docker2singularity.sh ubuntu:14.04
set -o errexit
set -o nounset
USAGE="Usage: docker2singularity [-m \"/mount_point1 /mount_point2\"] docker_image_name"
# --- Option processing --------------------------------------------
if [ $# == 0 ] ; then
echo $USAGE
exit 1;
fi
mount_points="/oasis /projects /scratch /local-scratch /work /home1 /corral-repl /corral-tacc /beegfs /share/PI /extra /data /oak"
while getopts ':hm:' option; do
case "$option" in
h) echo "$USAGE"
exit
;;
m) mount_points=$OPTARG
;;
:) printf "missing argument for -%s\n" "$OPTARG" >&2
echo "$usage" >&2
exit 1
;;
\?) printf "illegal option: -%s\n" "$OPTARG" >&2
echo "$usage" >&2
exit 1
;;
esac
done
shift $((OPTIND - 1))
image=$1
################################################################################
### CONTAINER RUNNING ID #######################################################
################################################################################
runningid=`docker run -d $image tail -f /dev/null`
# Full id looks like
# sha256:d59bdb51bb5c4fb7b2c8d90ae445e0720c169c553bcf553f67cb9dd208a4ec15
# Take the first 12 characters to get id of container
container_id=`echo ${runningid} | cut -c1-12`
# Network address, if needed
network_address=`docker inspect --format="{{.NetworkSettings.IPAddress}}" $container_id`
################################################################################
### IMAGE NAME #################################################################
################################################################################
image_name=`docker inspect --format="{{.Config.Image}}" $container_id`
# using bash substitution
# removing special chars [perhaps echo + sed would be better for other chars]
image_name=${image_name//\//_}
image_name=${image_name/:/_}
# following is the date of the container, not the docker image.
#creation_date=`docker inspect --format="{{.Created}}" $container_id`
creation_date=`docker inspect --format="{{.Created}}" $image`
################################################################################
### IMAGE SIZE #################################################################
################################################################################
size=`docker inspect --format="{{.Size}}" $image`
# convert size in MB (it seems too small for singularity containers ...?). Add 1MB to round up (minimum).
size=`echo $(($size/1000000+1))`
# adding half of the container size seems to work (do not know why exactly...?)
# I think it would be Ok by adding 1/3 of the size.
size=`echo $(($size+$size/4))`
echo "Size: $size MB for the singularity container"
################################################################################
### IMAGE CREATION #############################################################
################################################################################
TMPDIR=$(mktemp -u -d)
mkdir -p $TMPDIR
creation_date=`echo ${creation_date} | cut -c1-10`
new_container_name=/tmp/$image_name-$creation_date-$container_id.img
echo "(1/9) Creating an empty image..."
singularity create -s $size $new_container_name
echo "(2/9) Importing filesystem..."
docker export $container_id | singularity import $new_container_name
docker inspect $container_id >> $TMPDIR/singularity.json
singularity copy $new_container_name $TMPDIR/singularity.json /
# Bootstrap the image to set up scripts for environment setup
echo "(3/9) Bootstrapping..."
singularity bootstrap $new_container_name
chmod a+rw -R $TMPDIR
################################################################################
### SINGULARITY RUN SCRIPT #####################################################
################################################################################
echo "(4/9) Adding run script..."
CMD=$(docker inspect --format='{{json .Config.Cmd}}' $image)
if [[ $CMD != [* ]]; then
if [[ $CMD != "null" ]]; then
CMD="/bin/sh -c "$CMD
fi
fi
# Remove quotes, commas, and braces
CMD=`echo "${CMD//\"/}" | sed 's/\[//g' | sed 's/\]//g' | sed 's/,//g'`
ENTRYPOINT=$(docker inspect --format='{{json .Config.Entrypoint}}' $image)
if [[ $ENTRYPOINT != [* ]]; then
if [[ $ENTRYPOINT != "null" ]]; then
ENTRYPOINT="/bin/sh -c "$ENTRYPOINT
fi
fi
# Remove quotes, commas, and braces
ENTRYPOINT=`echo "${ENTRYPOINT//\"/}" | sed 's/\[//g' | sed 's/\]//g' | sed 's/,/ /g'`
echo '#!/bin/sh' > $TMPDIR/singularity
if [[ $ENTRYPOINT != "null" ]]; then
echo $ENTRYPOINT '$@' >> $TMPDIR/singularity;
else
if [[ $CMD != "null" ]]; then
echo $CMD '$@' >> $TMPDIR/singularity;
fi
fi
chmod +x $TMPDIR/singularity
singularity copy $new_container_name $TMPDIR/singularity /
################################################################################
### SINGULARITY ENVIRONMENT ####################################################
################################################################################
echo "(5/9) Setting ENV variables..."
docker run --rm --entrypoint="/usr/bin/env" $image > $TMPDIR/docker_environment
# don't include HOME and HOSTNAME - they mess with local config
sed -i '/^HOME/d' $TMPDIR/docker_environment
sed -i '/^HOSTNAME/d' $TMPDIR/docker_environment
sed -i 's/^/export /' $TMPDIR/docker_environment
# add quotes around the variable names
sed -i 's/=/="/' $TMPDIR/docker_environment
sed -i 's/$/"/' $TMPDIR/docker_environment
singularity copy $new_container_name $TMPDIR/docker_environment /
singularity exec --writable $new_container_name /bin/sh -c "echo '. /docker_environment' >> /environment"
rm -rf $TMPDIR
################################################################################
### Permissions ################################################################
################################################################################
if [ "${mount_points}" ]; then
echo "(6/9) Adding mount points..."
singularity exec --writable --contain $new_container_name /bin/sh -c "mkdir -p ${mount_points}"
else
echo "(6/9) Skipping mount points..."
fi
# making sure that any user can read and execute everything in the container
echo "(7/9) Fixing permissions..."
singularity exec --writable --contain $new_container_name /bin/sh -c "find /* -maxdepth 0 -not -path '/dev*' -not -path '/proc*' -not -path '/sys*' -exec chmod a+r -R '{}' \;"
buildname=$(head -n 1 /etc/issue)
if [[ $buildname =~ Buildroot|Alpine ]] ; then
# we're running on a Builroot container and need to use Busybox's find
echo "We're running on BusyBox/Buildroot"
singularity exec --writable --contain $new_container_name /bin/sh -c "find / -type f -or -type d -perm -u+x,o-x -not -path '/dev*' -not -path '/proc*' -not -path '/sys*' -exec chmod a+x '{}' \;"
else
echo "We're not running on BusyBox/Buildroot"
singularity exec --writable --contain $new_container_name /bin/sh -c "find / -executable -perm -u+x,o-x -not -path '/dev*' -not -path '/proc*' -not -path '/sys*' -exec chmod a+x '{}' \;"
fi
echo "(8/9) Stopping and removing the container..."
docker stop $container_id
docker rm $container_id
echo "(9/9) Moving the image to the output folder..."
rsync --info=progress2 /tmp/$image_name-$creation_date-$container_id.img /output/
c4science · Help