lordzappo/cmo

Modular bioinformatics pipelines for the CMO

For users of the luna cluster at MSKCC CMO

Add this to your ~/.profile to get access to the cmo_* and cmoflow_* tools:

# Set PATH to include MSKCC's bin of tools, if found
if [ -d "/opt/common/CentOS_6-dev/bin/current" ]; then
    PATH="/opt/common/CentOS_6-dev/bin/current:$PATH"
fi

# Set PATH to include MSKCC's bin of python tools, if found
if [ -d "/opt/common/CentOS_6-dev/python/python-2.7.10/bin" ]; then
    PATH="/opt/common/CentOS_6-dev/python/python-2.7.10/bin:$PATH"
fi

Documentation lives here, and running workflows can be tracked here.

For external users

Here is how to install these tools without sudo rights:

curl -LO https://github.com/mskcc/cmo/archive/master.zip
unzip master.zip
cd cmo-master
python setup.py install --user

Add this to your ~/.profile to get access to the cmo_* and cmoflow_* tools:

# Set PATH to include local python bin if found
if [ -d "$HOME/.local/bin" ]; then
    PATH="$HOME/.local/bin:$PATH"
fi

For all other users