Quick Start Guide¶
This guide will walk you through how to start using dolphinNext pipelines and creating new pipelines.
First off, you need to enter dolphinNext web page: https://dolphinnext.umassmed.edu/ and click Sign Up or Sign in with Google buttons. You will be asked to enter your institute information. An email will be sent to you upon verification of your information.
To run existing pipelines, you need to create run environment in profile section. To do so, click on the profile button at the top right of the screen, then you’ll notice several tabs as shown below.
Follow through the steps in profile page to create SSH Key (optionally, Amazon Key) and then specify the hosts you want to use in run environments section. Once you complete these steps, you’re now able to submit jobs to specifed hosts.
Before creating run environment, SSH Keys needed to be created in SSH Keys tab. If you want to create Amazon EC2 instances and submit your jobs to Amazon Cloud, then both SSH and Amazon Key are required before specifying run environment.
The easiest way to run pipeline is going to use main page by clicking the Biocore DolphinNext button at the top left of the screen. Now, you can investigate publicly available pipelines as shown at below and select the pipeline you want run by clicking Learn More button.
Once pipeline is loaded, you will notice “Run” button at the right top of the page.
This button opens new window where you can create new project by clicking “Create a Project” button. After entering and saving the name of the project, it will be added to your project list. Now you can select your project by clicking on the project as shown in the figure below.
You may proceed with entering run name which will be added to your run list of the project. Clicking “Save run” will redirect to “run page” where you can initiate your run.
In the header of the run page, you will notice the rocket icon and the title of the run.
Run status is monitored at the right part of the header. Initially, orange
Waiting button is shown. In order to initiate run, following data need to be entered:
For detailed information about adding files, you can check our tutorial video:Once all requirements are satisfied, ``Waiting`` button will turn in to green ``ready to run`` button as shown below.
You can initiate your run by clicking
ready to run button. Please go through run page for detailed explanation about each module is used.
The simpliest way to edit pipelines is creating a copy of the existing ones by clicking copy pipeline icon which is located just next to pipeline title.
Similarly you can create a copy of process by clicking copy process button on the top right of the process window.
Once you copied the pipeline/process, you will own all the permissions of your process/pipeline and you can easily modify and save on your version.