Install FAQs

  1. Most install issues can be solved with updating pip

    pip install --upgrade pip


    pip3 install --upgrade pip

  2. Linux: Do you want to continue? [Y/n] Abort.

    sudo xargs apt-get -y install < install/requirements.sys


    sudo xargs apt-get -y --force-yes install < install/requirements.sys

    WARNING: this will automatically install everything in the requirements.sys file.

  3. mysqlclient: OSError: mysql_config not found

    Make sure MySQL is installed and running before trying to install mysqlclient with pip.

  4. ImportError: No module named 'numpy'

    You must install numpy manually and then rerun pip install dlatk:

    pip install numpy

  5. Packaged datasets: To find the path to the data do the following (assuming everything installed properly) and replace with data

    python -c "import dlatk; print(dlatk.__file__)"

  6. mysqlclient does not install in conda

    conda install -c bioconda mysqlclient