1. Installation

1.1. Pre-requisites

  1. Run these commands to install the required packages on Ubuntu:

    # install OS packages
apt-get update
apt-get install \
    cmake \
    enchant \
    gcc \
    git \
    graphviz \
    openssh-client \
    pandoc \
    python \
    python-pip \
    wget

# install libgit2 (version in apt repository is old)
pushd /tmp
wget https://github.com/libgit2/libgit2/archive/v0.26.3.tar.gz -O /tmp/libgit2-0.26.3.tar.gz
tar -xvvf /tmp/libgit2-0.26.3.tar.gz
cd /tmp/libgit2-0.26.3
cmake .
make
make install
ldconfig
cd /tmp
export LIBGIT2=/usr/local
echo "" >> ~/.bashrc
echo "# libgit2" >> ~/.bashrc
echo "export LIBGIT2=/usr/local" >> ~/.bashrc
source ~/.bashrc
rm /tmp/libgit2-0.26.3.tar.gz
rm -r /tmp/libgit2-0.26.3
popd

  2. Run this command to upgrade pip and setuptools:

    pip install -U pip setuptools

  3. Optionally, create ~/.wc/karr_lab_build_utils.cfg to configure the package (see configuration options in karr_lab_build_utils/config/core.schema.cfg). We recommend that Karr Lab members start by copying the shared configuration file from karr_lab_build_config/karr_lab_build_utils.cfg.

  4. Optionally, create an SSH key for GitHub. This is needed to run tests using Docker and CircleCI.

    1. Create an SSH key and save it to ~/.ssh/id_rsa:

      ssh-keygen -t rsa -b 4096 -C "your_email@example.com"
eval $(ssh-agent -s)
ssh-add ~/.ssh/id_rsa

    2. Copy the contents of ~/.ssh/id_rsa.pub and use it to add your SSH key to GitHub following the instructions at https://help.github.com/articles/adding-a-new-ssh-key-to-your-github-account.

    3. Configure git to use SSH by saving the following to ~/.gitconfig:

      [url "ssh://git@github.com/"]
    insteadOf = https://github.com/

  5. Optionally install Docker by following the installation instructions in “An Introduction to Whole-Cell Modeling.” This is needed to run tests using Docker and CircleCI.

  6. Optionally, install the CircleCI command line tool by following the installation instructions in “An Introduction to Whole-Cell Modeling.” This is needed to run tests using CircleCI.

  7. Optionally, create a PyPI account at https://pypi.python.org. This is needed to upload packages to PyPI.

  8. Optionally, save your PyPI credentials to ~/.pypirc. This is needed to upload packages to PyPI.:

    [distutils]
index-servers =
    pypi

[pypi]
repository: https://upload.pypi.org/legacy/
username: <username>
password: <password>

1.2. Install the latest revision from GitHub

Run the following command to install the latest version from GitHub:

pip install git+https://github.com/KarrLab/sphinxcontrib-googleanalytics.git#egg=sphinxcontrib_googleanalytics
pip install git+https://github.com/KarrLab/pkg_utils.git#egg=pkg_utils
pip install git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils
pip install git+https://github.com/KarrLab/karr_lab_build_utils.git#egg=karr_lab_build_utils