SciClone - Quick Start Guide

SciClone is a workflow management system with a domain-specific language (DSL).

The DSL has simple syntax and a minimal set of keywords. The syntax has similarities to python’s syntax and indenting.

Scientists can write a workflow script using the visual elements offered in SciClone web interface.

Preparation

  1. Browse to http://sr-p2irc-big3.usask.ca
  2. Click "Login" from top-right corner.
  3. If you are not registered yet, click "Click here to register" link.
  4. Create an account.
  5. An email will be sent to your email address for confirmation. Please check email and confirm your account.
  6. Now log on to the system.

Practice Example Task: Quality Checking and Visualization of Gene Sequence Data

  1. Search "Check Quality" or FastQC in "Services" panel and double click it.
  2. Delete the data parameter and leave the cursor there.
  3. Search F3D6_S194_L001_R1_001.fastq in data sources and use right-click context menu to copy to editor.
  4. Your code editor should look like the following: 
    
fq_html = fastqc.CheckQuality('/public/MiSeq_SOP/F3D6_S194_L001_R1_001.fastq')
  5. Click "Run" from commands panel.
  6. A new item will be added to the top of "Job Histories" panel. Double click it.
  7. The output tab at the bottom will show the quality report of the sequence file. Click it to visualize on the browser.

Run Sample

  1. Navigate to right-bottom panel named Workflows.
  2. Double click ""Local Server: Merge-Align-Convert" workflow.
  3. This is a previously saved workflow.
  4. Your code editor should look like the following: 
    
fq_html = fastqc.CheckQuality('/public/MiSeq_SOP/F3D6_S194_L001_R1_001.fastq')
  5. Click "Run" from commands panel.
  6. A new item will be added to the top of "Job Histories" panel. Double click it.
  7. The output tab at the bottom will show the quality report of the sequence file. Click it to visualize on the browser.