CZI Computational Science Training Workshop: Testing Setup

This directory contains scripts for testing your machine to make sure you have the software you’ll need for your workshop installed. To use these scripts:

  1. Download swc-installation-test-1.py.

  2. Run it from the shell:

    $ python swc-installation-test-1.py
    Passed
    
  3. Download swc-installation-test-2.py.

  4. Run it from the shell:

    $ python swc-installation-test-2.py
    check virtual-shell...  pass
    ...
    Successes:
    
    virtual-shell Bourne Again Shell (bash) 4.2.37
    ...
    

    If you see something like:

    $ python swc-installation-test-2.py
    check virtual-shell...  fail
    ...
    check for command line shell (virtual-shell) failed:
      command line shell (virtual-shell) requires at least one of the following dependencies
      For instructions on installing an up-to-date version, see
      http://software-carpentry.org/setup/
      causes:
      check for Bourne Again Shell (bash) failed:
        could not find 'bash' executable for Bourne Again Shell (bash)
        For instructions on installing an up-to-date version, see
        http://software-carpentry.org/setup/
    ...
    

    follow the suggestions to try and install any missing software. For additional troubleshooting information, you can use the --verbose option:

    $ python swc-installation-test-2.py --verbose
    check virtual-shell...  fail
    ...
    ==================
    System information
    ==================
    os.name            : posix
    ...
    

    Data for tutorials

    Get it here

For Day Two:

  1. Follow the steps outlined here for your tutorial: https://chanzuckerberg.github.io/scRNA-python-workshop/intro/setup.html