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
Run this command to upgrade pip and setuptools:
pip install -U pip setuptools
~/.wc/karr_lab_build_utils.cfgto 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
Optionally, create an SSH key for GitHub. This is needed to run tests using Docker and CircleCI.
Create an SSH key and save it to
ssh-keygen -t rsa -b 4096 -C "email@example.com" eval $(ssh-agent -s) ssh-add ~/.ssh/id_rsa
Copy the contents of
~/.ssh/id_rsa.puband 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.
Configure git to use SSH by saving the following to
[url "ssh://firstname.lastname@example.org/"] insteadOf = https://github.com/
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.
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.
Optionally, create a PyPI account at https://pypi.python.org. This is needed to upload packages to PyPI.
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/log.git#egg=log 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