diff --git a/SIS/docker2singularity-master/Dockerfile b/SIS/docker2singularity-master/Dockerfile new file mode 100644 index 0000000..c31ef08 --- /dev/null +++ b/SIS/docker2singularity-master/Dockerfile @@ -0,0 +1,15 @@ +FROM docker:1.13 + +RUN apk add --update automake libtool m4 autoconf alpine-sdk linux-headers && \ + wget -qO- https://github.com/gmkurtzer/singularity/archive/2.1.2.tar.gz | tar zxv && \ + cd singularity-2.1.2 && ./autogen.sh && ./configure --prefix=/usr/local && make && make install && \ + cd ../ && rm -rf singularity-2.1.2 && \ + apk del automake libtool m4 autoconf alpine-sdk linux-headers + +RUN mkdir -p /usr/local/var/singularity/mnt + +RUN apk add e2fsprogs bash tar rsync +ADD docker2singularity.sh /docker2singularity.sh +RUN chmod a+x docker2singularity.sh + +ENTRYPOINT ["docker-entrypoint.sh", "/docker2singularity.sh"] diff --git a/SIS/docker2singularity-master/LICENSE b/SIS/docker2singularity-master/LICENSE new file mode 100644 index 0000000..8dada3e --- /dev/null +++ b/SIS/docker2singularity-master/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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Are you working on Mac or Windows with no easy access to a Linux machine? `docker2singularity` is the simplest way to generate Singularity images. Note that the upcoming Singularity (2.3) release supports import from Docker without sudo, natively, and this is the recommended approach. More information will be provided in the upcoming documentation for 2.3. + +## Requirements + + - Docker (native Linux or Docker for Mac or Docker for Windows) - to create the Singularity image. + - Singularity >= 2.1 - to run the Singularity image (**versions 2.0 and older are not supported!**). + +## Usage + +No need to download anything from this repository! Simply type: + + docker run \ + -v /var/run/docker.sock:/var/run/docker.sock \ + -v D:\host\path\where\to\output\singularity\image:/output \ + --privileged -t --rm \ + singularityware/docker2singularity \ + ubuntu:14.04 + +Replace `D:\host\path\where\to\output\singularity\image` with a path on the host filesystem where your Singularity image will be created. Replace `ubuntu:14.04` with the docker image name you wish to convert (it will be pulled from Docker Hub if it does not exist on your host system). + +`docker2singularity` uses the Docker daemon located on the host system. It will access the Docker image cache from the host system avoiding having to redownload images that are already present locally. + +## Tips for making Docker images compatible with Singularity + + - Define all environmental variables using the `ENV` instruction set. Do not rely on `.bashrc`, `.profile`, etc. + - Define an `ENTRYPOINT` instruction set pointing to the command line interface to your pipeline + - Do not define `CMD` - rely only on `ENTRYPOINT` + - You can interactively test the software inside the container by overriding the `ENTRYPOINT` + `docker run -i -t --entrypoint /bin/bash bids/example` + - Do not rely on being able to write anywhere other than the home folder and `/scratch`. Make sure your container runs with the `--read-only --tmpfs /run --tmpfs /tmp` parameters (this emulates the read-only behavior of Singularity) + - Don’t rely on having elevated user permissions + - Don’t use the USER instruction set + +## FAQ +### "client is newer than server" error +If you are getting the following error: +`docker: Error response from daemon: client is newer than server` + +You need to use the `docker info` command to check your docker version and use it to grab the correct corresponding version of `docker2singularity`. For example: + + docker run \ + -v /var/run/docker.sock:/var/run/docker.sock \ + -v D:\host\path\where\to\output\singularity\image:/output \ + --privileged -t --rm \ + singularityware/docker2singularity:1.11 \ + ubuntu:14.04 + +Currently only the 1.10, 1.11, 1.12, and 1.13 versions are supported. If you are using an older version of Docker you will need to upgrade. + +### My cluster/HPC requires Singularity images to include specific mount points +If you are getting `WARNING: Non existant bind point (directory) in container: '/shared_fs'` or a similar error when running your Singularity image that means that your Singularity images require custom mount points. To make the error go away you can specify the mount points required by your system when creating the Singularity image: + + docker run \ + -v /var/run/docker.sock:/var/run/docker.sock \ + -v D:\host\path\where\to\output\singularity\image:/output \ + --privileged -t --rm \ + singularityware/docker2singularity \ + -m "/shared_fs /custom_mountpoint2" \ + ubuntu:14.04 + +## Acknowledgements +This work is heavily based on the `docker2singularity` work done by [vsoch](https://github.com/vsoch) and [gmkurtzer](https://github.com/gmkurtzer). Hopefully most of the conversion code will be merged into Singularity in the future making this container even leaner! diff --git a/SIS/docker2singularity-master/docker2singularity.sh b/SIS/docker2singularity-master/docker2singularity.sh new file mode 100644 index 0000000..9ec16e9 --- /dev/null +++ b/SIS/docker2singularity-master/docker2singularity.sh @@ -0,0 +1,192 @@ +#! /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/ diff --git a/SIS/hello_world_pipeline_light/.dockerignore b/SIS/hello_world_pipeline_light/.dockerignore new file mode 100644 index 0000000..c291c09 --- /dev/null +++ b/SIS/hello_world_pipeline_light/.dockerignore @@ -0,0 +1 @@ +images diff --git a/SIS/hello_world_pipeline_light/Dockerfile b/SIS/hello_world_pipeline_light/Dockerfile new file mode 100644 index 0000000..2911b3c --- /dev/null +++ b/SIS/hello_world_pipeline_light/Dockerfile @@ -0,0 +1,11 @@ +FROM alpine:latest + +RUN apk update +RUN apk add python3 +RUN pip3 install --upgrade pip +RUN pip3 install snakemake + +RUN mkdir /pipeline +RUN mkdir /data + +ENTRYPOINT ["snakemake", "-q", "-s", " /pipeline/hello_world_pipeline.snake", "-d", "/data"] diff --git a/SIS/hello_world_pipeline_light/README.txt b/SIS/hello_world_pipeline_light/README.txt new file mode 100644 index 0000000..f81b1d0 --- /dev/null +++ b/SIS/hello_world_pipeline_light/README.txt @@ -0,0 +1,2 @@ +You can download the singularity container here: +https://polybox.ethz.ch/index.php/s/4CIiaRR4JogMZRy diff --git a/SIS/hello_world_pipeline_light/create_and_run_container_locally.sh b/SIS/hello_world_pipeline_light/create_and_run_container_locally.sh new file mode 100755 index 0000000..e3c0a3f --- /dev/null +++ b/SIS/hello_world_pipeline_light/create_and_run_container_locally.sh @@ -0,0 +1,14 @@ +#!/usr/bin/env bash +IMAGE_NAME=hello_world_pipeline_light +# remove old container +rm -rf ${IMAGE_NAME}*.img +# build the Docker container using the "Dockerfile" +sudo docker build -t ${IMAGE_NAME} . +# convert the Docker container to a Singularity image +#sudo docker run -v /var/run/docker.sock:/var/run/docker.sock -v $(pwd):/output --privileged -t --rm singularityware/docker2singularity ${IMAGE_NAME} +#./docker2singularity.sh ${IMAGE_NAME} +sudo docker run -v /var/run/docker.sock:/var/run/docker.sock -v $(pwd):/output --privileged -t --rm my_docker2_singularity ${IMAGE_NAME} +# rename the image +mv ${IMAGE_NAME}*.img ${IMAGE_NAME}.img +# run the image with some binding +singularity run -B ./pipeline:/pipeline -B ./data:/data ${IMAGE_NAME}.img diff --git a/SIS/hello_world_pipeline_light/pipeline/hello_world_pipeline.snake b/SIS/hello_world_pipeline_light/pipeline/hello_world_pipeline.snake new file mode 100644 index 0000000..a2cefe5 --- /dev/null +++ b/SIS/hello_world_pipeline_light/pipeline/hello_world_pipeline.snake @@ -0,0 +1,85 @@ +########################################## +## Basic hello world Snakemake pipeline ## +########################################## +# +# @author: Balazs Laurenczy +# @date: 2017 + + +######## +# INIT # +######## + +import os, logging + +from timeit import default_timer as t +from datetime import datetime + +# set up logging +logging.basicConfig(level = logging.INFO, format = '#%(asctime)s | %(levelname)-7s | %(filename)-20s: %(message)s') + +logging.info('Starting Snakemake pipeline ...') + +# get config parameters +N_FILES = int(config.get('n', 4)) + +OUT_FOLDER = config.get('output_folder', 'output') +if OUT_FOLDER[:-1] != '/': OUT_FOLDER += '/' # add ending slash to folder path + +REF_FOLDER = config.get('ref_folder', 'ref_output') +if REF_FOLDER[:-1] != '/': REF_FOLDER += '/' # add ending slash to folder path + + +######### +# RULES # +######### + +rule all: + input: + expand(OUT_FOLDER + 'helloworld_{w}.log', w = range(N_FILES)) + run: + logging.info('Pipeline completed.') + + +rule write_hello: + output: + OUT_FOLDER + 'hello_{w}.log' + shell: + 'echo "hello{wildcards.w}" > {output}' + + +rule write_world: + output: + OUT_FOLDER + 'world_{w}.log' + shell: + 'echo "world{wildcards.w}" > {output}' + + +rule write_hello_world: + input: + hello = OUT_FOLDER + 'hello_{w}.log', + world = OUT_FOLDER + 'world_{w}.log' + output: + OUT_FOLDER + 'helloworld_{w}.log' + shell: + 'cat {input.hello} {input.world} > {output}' + + +onsuccess: + logging.info('Pipeline completed successfully.') + + if not os.path.exists(REF_FOLDER): + exit('Cannot check validity of pipeline as there is no reference folder at path "{}". Aborting.'.format(REF_FOLDER)) + + # test if output folders are identical + shell('cd {OUT_FOLDER} && find . -regex ".*.log" -type f -exec md5sum {{}} \; | sort -k2 > content.md5') + try: + shell('diff {OUT_FOLDER}content.md5 {REF_FOLDER}content.md5') + logging.info('Pipeline is valid.'.format(REF_FOLDER)) + except Exception: + logging.error('Some differences (see above) exist between the current pipeline\'s output ' + + 'and the reference output at path "{}". Pipeline is *not* valid.'.format(REF_FOLDER)) + +onerror: + logging.info('Pipeline failed.') +