enormandeau / mreps_workflow

Extract interesting microsatellite markers using mreps and format them into a usable .tsv format

mreps_workflow

Extract interesting microsatellite markers from a reference genome with mreps and format them into a usable .tsv format

Dependencies

Linux

mreps_workflow has been tested on Linux (Ubuntu 12.04+). It may work on MacOSX but has not been tested.

mreps

A copy of mreps must be installed on your computer. A version of mreps is included with the workflow. Decompress the mreps archive and run make from the the new mreps foler. Then copy the mreps executable in your path, for example with:

sudo cp mreps /usr/local/bin

Installation

mreps_workflow is installed with the following command:

sudo make install

You must have administrative rights on the computer where you wish to install it. Alternatively, you can add the mreps_workflow directory to your $PATH variable. Launch the following command in the terminal for a one-shot use or add the same line to your ~/.bashrc file to make the change persistent.

export PATH=/path/to/mreps_workflow:$PATH

Testing the installation

To test the installation, move to the mreps_workflow directory and launch:

make test

Use

NOTE: Then contig names must not contain spaces. You can replace any spaces in the names by underscores (_).

Changing the mreps parameters

The mreps parameters must be adjusted in the mreps_workflow.sh script. You then need to run make install again so that the new parameters can be used.

Running mreps_workflow.sh

Launching mreps_workflow.sh is done with the following command:

mreps_workflow.sh fasta_filename.fasta

Contributions are welcome

If you find a bug or improve mreps_workflow, please contact the author.