TissueMAPS

Online documentation

For the moment, documentation is available at tissuemaps.org <http://tissuemaps.org/>_ and requires authentication. Use can login with your Github username.

Once repositories will be public, documentation will be hosted on Read the Docs <https://readthedocs.org/>_.

Installation of TissueMAPS Python packages during pre-release phase

The installation guide of the documentation already assumes that packages are available on PiPy <https://pypi.python.org/pypi>. For now, they still need to be installed from Github. This can get a bit tricky, because cloning private repositories require authentication. Best practice is to use SSH key-based authentication or deploy keys <https://developer.github.com/guides/managing-deploy-keys/#deploy-keys>. In addition, the setup.py files also already declare the packages as requirements that can be installed from PiPy.

You may find the following steps helpful:

• Create a SSH key-pair::

  ssh-keygen -f ~/.ssh/github

• Add the following lines to your ~/.ssh/config file::

  Host github

  HostName        github.com
  User            git
  IdentityFile    ~/.ssh/github

• Add the public key ~/.ssh/github.pub to your Github account, see Github docs <https://help.github.com/articles/adding-a-new-ssh-key-to-your-github-account/>_.

• After you have installed all non-Python dependencies as described in the installation guide, you can use the following script to create a virtual environment and install all TissueMAPS packages into it::

  !/bin/bash

  sudo pip install virtualenv virtualenvwrapper export WORKON_HOME=$HOME/.virtualenvs source /usr/local/bin/virtualenvwrapper.sh workon tissuemaps || mkvirtualenv tissuemaps

  if [[ $(python -mplatform | grep -i Ubuntu) ]] then LIB_DIR=$VIRTUALENVWRAPPER_HOOK_DIR/tissuemaps/lib/python2.7/site-packages if [ ! -e $LIB_DIR/cv2.so ] then ln -s /usr/local/lib/python2.7/dist-packages/cv2.so $LIB_DIR/cv2.so fi elif [[ $(python -mplatform | grep -i Darwin) ]] then if [ ! -e $LIB_DIR/opencv3.pth ] then ln -s /usr/local/lib/python2.7/site-packages/opencv3.pth $LIB_DIR/opencv3.pth fi else exit 1 fi

  git clone github:tissuemaps/gc3pie $HOME/gc3pie cd $HOME/gc3pie && pip install -e . && cd

  PACKAGES=(jtlibrary jtmodules tmlibrary tmserver) RELEASE="v0.1.0" for p in "${PACKAGES[@]}" do git clone github:tissuemaps/$p $HOME/$p cd $HOME/$p && git checkout $RELEASE && pip install -e . && cd done

• Packages can be either optained individually (as in the above script) or via the main TissueMAPS repository. Individual repositories will by default get checked out at the latest commit. If you want the current release version you need to checkout <https://git-scm.com/docs/git-checkout>_ tag v0.1.0. The main TissueMAPS repository contains the other repositories as submodules, which will automatically get checked out at the current release tag::

  git clone --recursive https://github.com/TissueMAPS/TissueMAPS.git ~/tissuemaps