The ISA (Investigation, Study, Assay) metadata framework (https://isa-tools.org/) can be used to describe experimental metadata readable for both humans and machines (using ontologies). ISA-Tab and ISA-JSON files can be created, read and edited using the ISA-API (https://github.com/ISA-tools/isa-api).

The steps below describe how to create a conda environment with the isatools Python package in the DRE.

Prerequisites

Install conda for all users (download from https://docs.conda.io/en/latest/miniconda.html) and open the respective ports as described in https://support.mydre.org/portal/en/kb/articles/python#Basic_install.

Create conda environment

1. Open Anaconda Prompt (Miniconda3)

2. Create new environment named py36isa

   Use Python 3.6 (Python >3.6 resulted in errors related to pandas).

   conda create -n py36isa python=3.6
   

3. Activate environment

   conda activate py36isa
   

4. Install isatools (Python ISA-API)

   conda install -c bioconda isatools
   

5. Install Jupyter notebook and kernel

   conda install jupyter 
   conda install ipykernel
   

6. Disable Python user site packages

   This is enabled per default, but causes errors with numpy.

   conda env config vars set PYTHONNOUSERSITE=1
   

7. Register environment (for user)

   ipython kernel install --user --name=py36isa --display-name "Python3.6 (py36isa)"
   

8. Run Jupyter notebook

   jupyter notebook
   

   Preferably, open the provided link - http://127.0.0.1:8888/?token=<insert_token_from_command_line> - in chrome.