Quick Start Guide

This guide will walk you through how to start using dolphinNext pipelines and creating new pipelines.

Short Overview


Getting Started

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.

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Creating Profile


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.

../_images/profile_tabs2.png

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.

Note

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.

Running Pipelines


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.

../_images/main_page.png

Once pipeline is loaded, you will notice “Run” button at the right top of the page.

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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.

../_images/project_pipeselect.png

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.

Run Page

In the header of the run page, you will notice the rocket icon and the title of the run.

../_images/run_header_waiting.png

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:

  1. Work Directory: Full path of the directory, where nextflow runs will be executed.
  2. Run Environment: Profile that is created in the profile page. If Amazon profile is selected, then status of the profile should to be at the stage of running.
  3. Inputs: Value and path of the files need to be entered.
../_images/run_params.png

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.../_images/run_header_ready.png

You can initiate your run by clicking ready to run button. Please go through run page for detailed explanation about each module is used.

Editing Processes/Pipelines

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.

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Similarly you can create a copy of process by clicking copy process button on the top right of the process window.

../_images/copy_process.png

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.

Creating New Pipelines/Processes

Please follow through the Pipeline Guide to create new pipelines and Process Guide for processes. You can also check our developer guide video to start: