Installation
Follow the link: https://github.com/KarchinLab/SCHISM/tree/dev/conda
You can download the installation bundle corresponding to the most recent stable release of SCHISM from
Please make sure that you have all the dependencies listed below on your system.
Usage example files are available at:
Under certain circumstances, Mac or Windows users may find it more convenient to run SCHISM inside a docker container. A docker image of an ubuntu environment with SCHISM installed is made available with every package release.
To run SCHISM from a docker container, please make sure that you have Docker-Toolbox installed on your machine. Next, initiate a docker quickstart terminal.
Please download the desired SCHISM docker image from here, and from the command line call
# decompress the docker image
gunzip SCHISM-1.1.0.docker-image.tar.gz
# load the image in the docker image list. This step may take a minute.
docker load < SCHISM-1.1.0.docker-image.tar
Now with the docker image ready, it is convenient to generate an alias when making calls to runSchism runner script. Using this alias, you can run SCHISM in a docker container with minimal syntax change. From the command line,
# First, create a docker container from the distributed docker image.
docker run -d --name schism_bash -i -t -v /path/to/working/dir/:/path/to/working/dir/ schism:1.1.0 bash
# generate a command line alias for runSchism runner script.
# Substitute the /path/to/working/dir to point to the directory where
# run results will be stored in both instances.
# This is typically the same directory where the configuration file resides.
dockerRunSchism="docker exec schism_bash runSchism"
At this point, you make calls to runSchism as usual, but substitute 'runSchism' with dockerRunSchism. For instance
$dockerRunSchism analyze -c /path/to/working/dir/experiment.yaml
will be the equivalent of runSchism analyze -c /path/to/working/dir/experiment.yaml, run inside a container.
You can install SCHISM by making the call below from your system's command line.
pip install SCHISM-1.1.0.tar.gz
Please note that if you download the bundle from Github release page (as opposed to karchinlab website), you need to run the following step before the pip install step above.
# make source distribution
python setup.py sdist
# now pip install from source distribution
pip install dist/SCHISM-1.1.0.tar.gz
Once the installation finishes, you can confirm that schism was successfully installed by calling:
python -c "import SCHISM; print SCHISM.__version__"
from your command line. The above command should print out the SCHISM version you have installed.
The runSchism master script should be available on your system path. You can verify this by running:
which runSchism
runSchism --help
Finally, a template SCHISM configuration file is included in installation tar ball uder /data.
Decompress the installation bundle in the desired destination directory. Make sure that the destination directory is present on your system's PATH. Then, you can call
runSchism --help
Alternatively, SCHISM can be installed in user home directory, where system-wide privileges are not available.
pip install --user dist/SCHISM-1.1.0.tar.gz
As mentioned above, a template SCHISM configuration file is included in the installation bundle under /data.
- numpy >= 1.7.1
- scipy >= 0.12.0
- matplotlib >= 1.2.0
- PyYAML >= 3.11
- python-igraph >= 0.7.0 (required for consensus tree visualization)
- sklearn >= 0.14
Please note that using the command suggested for system-wide installation ensures that all the above dependencies are available on your system, with the exception of python-igraph.
To install python-igraph, please follow the directions here which cover python-igraph dependencies (Cairo, Pycairo and igraph C core).
Disclaimer: If your system does not meet the requirements for neither numpy nor scipy, the pip install command will fail due to installation dependency of scipy on numpy (known issue here). In this case, a work-around is to pip install numpy first and then proceed to SCHISM installation.