Quick Start Guide

This guide will walk you through how to starty using dolphin workflows.

!!! Warning: Dolphin docker aimed for developers. If you are going to use dolphin, please use `Quick Start Guide for UI http://dolphin.readthedocs.io/en/master/dolphin-ui/quickstart.html`_ section !!!

General

Clone the docker first: https://github.com/UMMS-Biocore/dolphin-docker

Building dolphin-docker

First we need to build dolphin-docker image. Please go to the cloned directory.

cd your_path/dolphin-docker

docker build -t dolphin-docker .

Creating an export directory in your host

dolphin-docker uses a directory in your host system to hold information when you exit your docker container. If you are using boot2docker please connect your VM with

boot2docker ssh

create your export directory and give the full permissions that are going to be used by the container.

sudo mkdir /mnt/sda1/export

sudo chmod 777 /mnt/sda1/export

Running dolphin-docker

Dolphin docker has a apache web server that will be used on port 8080 if you run like below.

docker run -p 8080:80 -v /mnt/sda1/export:/export -ti dolphin-docker /bin/bash

or you can pull latest stable build

docker run -p 8080:80 -v /mnt/sda1/export:/export -ti nephantes/dolphin-docker /bin/bash

Initialize the system

You need to initialize the system using ‘startup’ command. This will prepare example genome and mysql database in /export directory that are going to be used by dolphin in the first run.

Starting mysql and web server

‘startup’ command will also start mysql and apache web servers. When you run dolphin-docker container. You need to start start using this command.

To reach the applications on apache server please add your docker host ip address into /etc/hosts file

Ex:

echo ${DOCKER_HOST}

tcp://192.168.59.103:2376

/etc/hosts =>

192.168.59.103 dolphin.umassmed.edu

Now you can use your browser to reach the website using

For phpmyadmin

Running a test workflow

To run a test workflow please go to directory below;

cd /usr/local/share/dolphin_tools/test/

./run.bash w1.txt

Creating needed password variables

After installing dolphin-ui within docker, you are going to want to create a ”.salt” file in your config folder with it’s contents similar to this:

[Dolphin]
SALT=
PEPPER=
MASTER=
AMAZON=

Make sure you fill in the values for each of these variables with your desired passphrases.

These variables are used for specific passcodes to encrypt and decrypt valuable information that you would want to protect.