pupster90/indra repository overview

⁠Introduction

This virtual machine (VM) can be used for running indra. Specifically, this is used by the NDEX and Sorger Lab team to develop new functionalities to Indra. Later we will make an easier non-development version.

⁠Installation and Use

First, you must install docker. Windows users, instead of installing docker install docker toolbox⁠. Follow this link⁠ for installation instructions:

Downloading the VM, is equivalent to pulling the docker image (downloads can take a while). To do this open your terminal and type: sudo docker pull pupster90/indra

To enter the VM, you create a container of the indra image by typing: sudo docker run -it -p 8888:8888 -v /decide/a/path:/root/Documents pupster90/indra

In the code above /decide/a/path can be any directory path you like. This allows you to access and edit any folder (as specified /decide/a/path) on your computer from within the VM (at /root/Documents).

Since this is the development version, we install the indra source code instead of using pip. We do this by using github⁠. You can either install the main indra repository⁠ or you can make a fork⁠. Once inside the VM you can create a copy of a repository to /decide/a/path like so: cd ~/Documents git clone https://github.com/pupster90/indra.git

The VM also allows you to edit any file in decide/a/path using Jupyter. To run Jupyter at http://localhost:8888⁠ type: jupyter notebook

⁠Versions

The Tags⁠ tab shows all the versions of the Indra image. By default you install the most recent version. The pre are versions that were not yet completely functional. We where give summarize the versions:

• 6 Installed jupyterlab⁠
• 5 installed python package redis (with pip) and google.datastore⁠
• 4 installed python package ndex (with pip)
• 2 Added nb_extensions to jupyter
• 1 installed all the python packages: cython(0.23.5), jnius-indra, pygraphviz, future, objectpath, kappy, pysb, pybel, matplotlib, ndex2, and rdflib
• pre2 installed Java 8, and setup the JAVA_HOME path. Java Version: openjdk version "1.8.0_162"
• pre1 this is simply ubuntu18 with Anaconda installed

⁠Comments

If you have any issues or notice a bugs, please feel free to leave a comment!