Initial commit.

.gitignore

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+.DS_Store
+*~

README.md

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+# docker2singularity
+This script exports a [Docker](https://www.docker.com/) image as a [Singularity](https://sylabs.io/singularity/) `.sif` file. This can be useful for porting Dockerized code to run on shared user systems like clusters, which sometimes run Singularity rather than Docker.
+
+# Prerequisites
+- Install Docker (tested with `20.10.6`)
+
+# Usage
+1. Build or pull the Docker image you wish to export to a Singularity `.sif` file
+
+	```bash
+	docker pull ubuntu:latest
+	```
+
+2. Run `docker2sif.sh` to export the image as a `.sif` file
+
+	```bash
+	cd docker2singularity
+	./docker2singularity.sh ubuntu
+	```
+
+	This should write a file called `ubuntu.sif` in the current working directory, e.g., `docker2singularity/ubuntu.sif`
+
+	Optionally, you can specify where to save the output `.sif` file:
+
+	```bash
+	./docker2singularity.sh ubuntu $HOME/ubuntu_singularity.sif
+	```
+	#### Expected Output
+	If it worked, you'll see output similiar to the following:
+
+	```bash
+	Exporting docker image ubuntu --> /Users/giarrmn1/ubuntu_singularity.sif 
+
+	Image Format: squashfs
+	Docker Image: ubuntu
+	Container Name: ubuntu_singularity.sif
+
+	Inspected Size: 73 MB
+
+	(1/10) Creating a build sandbox...
+	(2/10) Exporting filesystem...
+	(3/10) Creating labels...
+	(4/10) Adding run script...
+	(5/10) Setting ENV variables...
+	(6/10) Adding mount points...
+	(7/10) Fixing permissions...
+	(8/10) Stopping and removing the container...
+	(9/10) Building squashfs container...
+	INFO:    Starting build...
+	INFO:    Creating SIF file...
+	INFO:    Build complete: /tmp/ubuntu_singularity.sif
+	(10/10) Moving the image to the output folder...
+	     27,717,632 100%   80.25MB/s    0:00:00 (xfr#1, to-chk=0/1)
+	Final Size: 27MB
+	 Exported Docker image ubuntu --> /Users/giarrmn1/ubuntu_singularity.sif 
+
+	```
+
+	#### Help
+	Run `./docker2singularity -h` to print the help screen, including usage.
+
+	# Caveats
+	-  The docker image you wish to export must be available locally, i.e., you need to have built the image before you can export it to `.sif`. There's no reason we couldn't go straight from `Dockerfile` to `.sif` by including the option to `docker build` in the script, but we haven't implemented that yet.
+

docker2singularity.sh

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+#!/bin/bash
+# Export Docker image as Singularity .sif file
+# Maintainer: Matthew N. Giarra <[email protected]>
+# First commit 2021-06-10
+
+# Colors for printing
+DIR='\033[95m'
+OKBLUE='\033[94m'
+OKCYAN='\033[96m'
+OKGREEN='\033[92m'
+ENDC='\033[0m'
+BOLD='\033[1m'
+UNDERLINE='\033[4m'
+WARNING='\033[93m'
+FAIL='\033[91m'
+
+# Color to print on success
+SUCCESS=$OKCYAN
+
+# Function to display help
+display_help(){
+    echo -e "$SUCCESS $(basename $0): export docker image as a singularity .sif image file"
+    echo "   Usage: $(basename $0) <docker_image_name>"
+    echo "   Usage: $(basename $0) <docker_image_name> <sif_path_out>"
+    echo "   Example: "
+    echo "      docker pull ubuntu:latest"
+    echo "      ./$(basename $0) ubuntu ubuntu.sif"
+    echo "   Note: run \"docker image ls\" to print available docker images"
+    echo -e "$ENDC"
+    exit
+}
+
+# Display help if no inputs are supplied
+if [ $# -eq 0 ]; then
+    display_help
+fi
+
+# Display help if -h or --h is supplied as the only input
+while true; do
+    case "$1" in
+        -h | --help)
+            display_help;;
+        *)
+            break;;
+    esac
+done
+
+# Tag of the docker image to export as Singularity .sif file
+IMAGE_NAME_IN="$1"
+
+# Make sure the image exists so that we can print an informative message if it doesn't
+MATCHING_IMAGES=$(docker images -q $IMAGE_NAME_IN)
+if [ -z $MATCHING_IMAGES ]; then
+    echo -e "$FAIL Error: $IMAGE_NAME_IN does not appear to be a locally-available docker image"
+    echo -e "Available docker image tags:"
+    echo -e "$(docker images | tail -n +2 | awk '{print $1}')"
+    echo -e " Hint: run \"docker image ls\" to print available docker images $ENDC"
+    exit
+fi
+
+if [ $# -ge 2 ]; then
+    # User-specified output path for .sif file
+    IMAGE_PATH_OUT="$2"
+else
+    # Default to .sif file with same name as docker tag
+    IMAGE_PATH_OUT="$IMAGE_NAME_IN.sif"
+fi
+
+# Path to the output directory
+OUT_DIR=$(dirname "$IMAGE_PATH_OUT")
+
+# Make the output directory if it doesn't exist
+if [ ! -d "$OUT_DIR" ]; then
+    mkdir -p "$OUT_DIR"
+    if [ -d "$OUT_DIR" ]; then
+        echo -e "$SUCCESS Created directory $DIR$OUT_DIR $ENDC"
+    else
+        echo -e "$FAIL Error: could not create directory $DIR$OUT_DIR $ENDC"
+        exit 
+    fi 
+fi
+
+# Absolute path to output directory
+OUT_DIR_ABS=$(cd "$OUT_DIR"; pwd)
+
+# Name of the output image
+IMAGE_NAME_OUT=$(basename "$IMAGE_PATH_OUT")
+
+# Absolute path to the output file
+IMAGE_PATH_OUT_ABS="$OUT_DIR_ABS/$IMAGE_NAME_OUT"
+
+# If the output file exists, ask if we want to overwrite it
+if [ -f "$IMAGE_PATH_OUT_ABS" ]; then
+    while true; do
+        echo -e "$DIR$IMAGE_PATH_OUT_ABS$WARNING exists. Overwrite [y/N]? $ENDC"
+        read -p "" yn
+        case $yn in
+            [Yy]* ) break;;
+            [Nn]* ) exit;;
+            * ) exit;;
+        esac
+    done
+fi
+
+# Backup sif file if it already exists
+if [ -f "$IMAGE_PATH_OUT_ABS" ]; then
+    IMAGE_PATH_ABS_BACKUP="$IMAGE_PATH_OUT_ABS.backup"
+    mv "$IMAGE_PATH_OUT_ABS" "$IMAGE_PATH_ABS_BACKUP"
+
+    if [ -f "$IMAGE_PATH_ABS_BACKUP" ]; then
+        echo -e "$SUCCESS Backed up $DIR$IMAGE_PATH_OUT_ABS $SUCCESS-->$DIR $IMAGE_PATH_ABS_BACKUP $ENDC"
+    fi
+fi
+
+# Inform the user that we're about to execute the export
+echo -e "$SUCCESS Exporting docker image $DIR$IMAGE_NAME_IN $SUCCESS--> $DIR$IMAGE_PATH_OUT_ABS $ENDC"
+
+# Export the docker image to a Singularity .sif file
+docker run -v /var/run/docker.sock:/var/run/docker.sock -v "$OUT_DIR_ABS":/output -it --rm quay.io/singularity/docker2singularity --name $IMAGE_NAME_OUT $IMAGE_NAME_IN
+
+# Check that the sif file actually got saved
+if [ -f "$IMAGE_PATH_OUT_ABS" ]; then
+    echo -e "$SUCCESS Exported Docker image $IMAGE_NAME_IN --> $DIR$IMAGE_PATH_OUT_ABS $ENDC"
+
+    # Remove the backup image
+    if [ -f "$IMAGE_PATH_ABS_BACKUP" ]; then
+        rm "$IMAGE_PATH_ABS_BACKUP"
+    fi
+
+else
+    # Replace the image with the backup image
+    if [ -f "$IMAGE_PATH_ABS_BACKUP" ]; then
+        echo -e "$WARNING Canceled exporting $DIR$IMAGE_NAME_IN $WARNING--> $DIR$IMAGE_PATH_OUT_ABS$ENDC"
+        mv "$IMAGE_PATH_ABS_BACKUP" "$IMAGE_PATH_OUT_ABS"
+    else
+        echo -e "$FAIL Warning: $DIR$IMAGE_PATH_OUT_ABS$FAIL not found; exporting docker image $IMAGE_NAME_IN --> $DIR$IMAGE_PATH_OUT_ABS$FAIL appears to have failed. $ENDC"
+    fi
+fi