Grape Buildout

This buildout configures Grape pipelines, used for processing and analyzing RNA-Seq data.

• Download it from the Grape Homepage

To install it, check out the installation instructions:

• Installing the Grape Buildout

You have two options to evaluate Grape, one for a predefined dataset, and one for the case that you have a dataset for one of the species we provide genomes and annotations for.

• Test Grape with a predefined minimal test dataset
• Quickly test Grape with one of your your own datasets

In order to take full advantage of Grape, you need to learn how to configure and run it for all your RNA-Seq datasets.

• Customize Grape for your own datasets

The next step is to visualize the results in a web browser and share your results using the Raisin web server:

• Run the Raisin web server to visualize Grape results

Contents:

• Installing the Grape Buildout
  • Dependencies
• Test Grape with a predefined minimal test dataset
• Quickly test Grape with one of your your own datasets
  • Create databases for your project
  • Run the buildout
  • Run the pipeline
• Customize Grape for your own datasets
  • Choosing a project name
  • Layout
  • Configure the buildout.cfg
  • Adding a configuration file for the accessions
  • Adding a configuration file for the profile
  • Configuring the profile
  • Configuring the accessions
  • Create databases for your project
  • Run the buildout
  • Run the first pipeline
  • Run the other pipeline
• Run the Raisin web server to visualize Grape results

Indices and tables

• Index
• Module Index
• Search Page