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 !!!
First we need to build dolphin-docker image. Please go to the cloned directory.
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
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
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
Running a test workflow¶
To run a test workflow please go to directory below;
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.