Shock

Shock is actively being developed at github.com/MG-RAST/Shock.

Building

To build Shock manually, use the Makefile. Note that you need golang (>=1.6.0).

Docker

You can get the Shock Dockerimage with:

docker pull mgrast/shock

Or, to build the Docker image on you own:

git clone --recursive https://github.com/MG-RAST/Shock.git
cd Shock
docker build --force-rm --no-cache --rm -t mgrast/shock .

If you only need the statically compiled binary, you can extract it from the Dockerimage:

docker create --name shock mgrast/shock
mkdir -p bin
docker cp shock:/go/bin/shock-server ./bin/
docker cp shock:/go/bin/shock-client ./bin/
docker rm shock

MongoDB

In ubuntu you can simply install mongo with:

sudo apt-get install -y mongodb-server

If you do not want to use a package manager to install mongodb, use:

curl -s http://downloads.mongodb.org/linux/mongodb-linux-x86_64-2.4.14.tgz | tar -v -C /mongodb/ -xz

If you do not use a service manager such as systemd, you can start mongodb like this, in foreground:

/mongodb/bin/mongod --dbpath /data/

or in background:

nohup /mongodb/bin/mongod --dbpath /mnt/db/ &

You can also run MongoDB in a docker container:

mkdir -p /mnt/shock-server/mongodb
export DATADIR="/mnt/shock-server"
docker run --rm --name shock-server-mongodb -v ${DATADIR}/mongodb:/data/db --expose=27017 mongo mongod --dbpath /data/db

Configuration

The Shock configuration file is in INI file format. There is a template of the config file located at the root level of the repository.

Running

To run:

shock-server -conf <path_to_config_file>

With docker:

mkdir -p /mnt/shock-server/log
mkdir -p /mnt/shock-server/data
export DATADIR="/mnt/shock-server"
docker run --rm --name shock-server -p 7445:7445 -v ${DATADIR}/shock-server.cfg:/shock-config/shock-server.cfg -v ${DATADIR}/log:/var/log/shock -v ${DATADIR}/data:/usr/local/shock --link=shock-server-mongodb:mongodb mgrast/shock /go/bin/shock-server --conf /shock-config/shock-server.cfg

Comments:
port 7445: Shock server API (default in config)
“-v” mounts host to container directories
“–link” connects Shock server and mongodb (–link=$imagename:$alias) so you need to put the alias (in the example “mongodb”) as the value of the hosts variable in the shock-server.cfg

Documentation

For further information about Shock’s functionality, please refer to our github.

Developer Notes

To update vendor directory use the tool govendor: go get -u github.com/kardianos/govendor

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