README.md

Biomhandler

About

A python script to convert hdf5 biom files to json. Used in Phinch. We use PyInstaller to package that script into a standablone executable. Follow these steps to generate the executable:

Requirements

• Python 2 (https://wiki.python.org/moin/BeginnersGuide/Download)
• Pip (https://pip.pypa.io/en/stable/installing/)
• Virtualenv (https://virtualenv.pypa.io/en/stable/installation.html)

Install

First, clone the repo via git:

git clone https://github.com/PhinchApp/biomhandler.git

Then, create and active a python virtual environment:

cd biomhandler
virtualenv ./virtualenv
source ./virtualenv/bin/activate

Or, on Windows:

cd biomhandler
virtualenv ./virtualenv
./virtualenv/Scripts/activate

Finally, install dependencies:

cat requirements.txt | xargs -n 1 -L 1 pip install

Or, on Windows:

cat requirements.txt | %{pip install $_}

Packaging

The repository includes a pyinstaller specfile which tells pyinstaller how to create a standalone executable from the script. The resulting executable will be output at /dist/biomhandler. More information on pyinstaller.

If you're on a windows system edit biomhandler.spec before packaging so that the pathex argument to the Analysis function points to scipy's extra-dll folder. It should look something like this:

pathex=['C:/Users/pitch/Documents/biomhandler/virtualenv/Lib/site-packages/scipy/extra-dll']

To package, run:

pyinstaller biomhandler.spec

Usage

Using Python:

python biomhandler.py path-to-hdf5-biom-file

Using the standablone executable:

./dist/biomhandler path-to-hdf5-biom-file

License

The BSD 2-Clause License