Installation

For advanced users we recommend installing Teaser directly on your PC or cluster. This is required for adding new reference genomes, parameter sets or mappers. The included installation script install.py will download and compile a pre-configurated set of read mappers and read simulators.

Requirements:

• UNIX-like Operating System
• Python 2.x (should be in PATH as python)
• Internet connection for downloading mappers during install

Packages that may need to be installed before downloading and installing Teaser:

• python-pip (should be in PATH as pip)
• python-dev

Packages that may be needed for the automatic building of mapper binaries:

• build-essentials (gcc,g++,etc.)
• cmake
• zlib

Installation:

git clone https://github.com/Cibiv/Teaser.git
cd Teaser
./install.py

If any errors occur, the script will list all items that failed to install. If compilation for a mapper or simulator failed, it may be worth trying to manually download/compile it and place the executable files in the expected path in the software directory (The expected locations of mapper executable files can be found in the setups/base_mappers.yaml file).

Example Usage:

• To test if everything is working after the installation, you can try benchmarking mappers for a pre-defined E. coli dataset using the following command:

./teaser.py example_ecoli.yaml

Results will be placed in the reports directory.

(For more information on running Teaser from the command line, see Command Line).

• To start the local web server which allows using Teaser in your browser, run:

./server.py

(For more information on how to use the web browser interface, see Web Browser Interface).