This repo uses submodules so to download it, type the following

git clone --recursive https://github.com/iqbal-lab/Mykrobe-predictor.git

Then run the following command to compile libraries.

sh install.sh

To compile for S.aureus, run the following command

make STAPH=1 predictor

to create this executable

bin/Mykrobe.predictor.staph

To compile for M.tuberculosis, run the following command

make TB=1 predictor

to create this executable

bin/Mykrobe.predictor.tb

[In order to install on Mac you may need to install gcc via homebrew or macports. Running "gcc -v" should return something like: "gcc version 4.9.2 (Homebrew gcc49 4.9.2_1)" not "Apple LLVM version 6.0 (clang-600.0.57)"

Standard usage

Mykrobe.predictor.staph --file some_file.fastq --install_dir /path/to/Mykrobe-predictor

Finally, there are GUI versions of Mykrobe-predictor for Windows and Mac OS X, which you can download from Releases

We have a preprint of the paper describing Mykrobe predictor here: http://biorxiv.org/content/early/2015/04/26/018564 Please cite us if you use Mykrobe predictor in a publication

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