With Bioconda [Recommended]¶
conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge conda create -n concoct_env python=3 concoct
Note for Mac OSX users¶
Currently concoct on Mac OSX can only run in single threaded mode, which drastically increases the runtime. However, the Mac OSX installation of concoct can still be useful for testing purposes and is possible to install through conda as shown above.
The conda installation should be enough for most users. However, if you want to modify the source code, a manual installation might be needed. An example of a manual installation on an Ubuntu system can be seen in the Travis CI config file.
We provide a Docker image: binpro/concoct_latest which contains CONCOCT and its dependencies for a basic workflow.
Assuming DOcker is installed, the following command will then download the image from the Docker image index, map the Data folder to the image and log you into the docker image.
docker run -v /home/USER/Data:/opt/Data -i -t binpro/concoct_latest bash
To test concoct you can then do:
$ cd /opt/CONCOCT_latest $ nosetests
Which should execute all tests without errors.