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Installing svtools

Table of Contents

  1. Run from a docker image
  2. Preparing your Python environment
  3. Installing from PyPI using pip
  4. Installing directly from the git repo
  5. Installing from a github release tarball

Running from a docker image

Instead of installing, you can run svtools from a docker image, provided on dockerhub. The executable is in /opt/hall-lab/python-*/bin/svtools.

Preparing your Python environment

svtools requires Python 2.7. We recommend that you manage your installation with the pip package manager as shown below. Using pip will allow you to uninstall svtools easily. You might want to use pyenv virtualenv to create a virtual environment. There are instructions for setting up a virtualenv on the pyenv github site. pyenv installs pip by default.

The creation of the pyenv virtual environment and activation looks like this:

pyenv virtualenv 2.7.11 svtools
pyenv activate svtools

Installing from PyPI using pip

Once you have your Python environment set up you should be able to install the svtools package from PyPI:

pip install svtools

You can spot check your svtools install by running:

svtools --version

Installing directly from the git repo

Once you have your Python environment set up you will want to clone svtools from the hall-lab github repository.

git clone https://github.com/hall-lab/svtools.git svtools_test
cd svtools_test

Or you can discover the release tags on the repo and checkout the latest version

git tag -l

when you discover the version tag you wish to install you can switch to that version using

git checkout tags/v0.2.0b1

note: you can ignore the warning about "You are in 'detached HEAD' state."

OR, you can just proceed to install from master.

We can use pip to install svtools from within the repo. If you are not already in the directory

cd svtools_test

or just

pip install .

Finally we can spot check our svtools installation and observe the version number.

svtools --version

Installing from a github release tarball

Once you have your python environment set up, visit the svtools releases github page. Select the latest release and use the Source code (tar.gz) link to download a tarball of the source.

Navigate to the download location on your filesystem and use the tar command:

tar -xvzf svtools-0.2.0b1.tar.gz

to expand the archive. While you wait, enjoy this cartoon from xkcd.

Now enter the directory that has been created.

cd svtools-0.2.0b1
pip install .

Installing the dependencies can take a few minutes, please be patient!

Finally we can spot check our svtools installation and observe the version number with the following command:

svtools --version