Installation

Download

You can do it from our GitHub repository in two different ways:

  1. Go to the releases tab and download the latest release.
  2. Clone the git repository in case you want the latest version of the code:
# Move into the folder in which you want to clone the repositoy.
$ cd ~/apps
# Clone it.
$ git clone https://github.com/Chimera-tools/ChimPipe.git

ChimPipe does not require any further installation step. It already comes with precompiled gemtools binaries. It is written in Bash and Awk and can be run as a standalone application on diverse Linux systems.

Requirements

Hardware:

  • 64-bits CPU.
  • RAM: ~40G for 100 million illumina paired-end reads.

Software:

  • 64-bit Linux System.
  • Bedtools v2.20.1 or higher.
  • Samtools v0.1.19 or higher.
  • Blast v2.2.29+ or higher (only if you want to generate your own similarity text files, see Gene pair similarity file in the Manual section).