GRABSEEDS: How to install

GRABSEEDS make heavy use of image manipulation and text recognition libraries and software. Please be patient and install the dependencies listed below.

External dependencies

• ImageMagick
  • libmagickwand-dev for APT on Debian/Ubuntu
  • ImageMagick-devel for Yum on CentOS
• tesseract-ocr
  • Make sure that you can run tesseract on the command line (i.e. in your PATH).

Python dependencies

• scipy
• matplotlib
• scikit-image
• pypdf2
• wand
• jcvi

Most of these Python libraries can be installed using easy_install or pip install, for example:

easy_install scipy matplotlib scikit-image pypdf2 wand jcvi

If you have problem installing the jcvi library, you can clone the jcvi repository directly and put the directory on your PYTHONPATH. For example, if you want to install it to ~/code, do the following:

$ cd ~/code
$ git clone git://github.com/tanghaibao/jcvi.git
$ export PYTHONPATH=~/code:$PYTHONPATH

To avoid setting PYTHONPATH everytime, please insert the last command in your .bashrc or .bash_profile.

Test

Download the test image below (right click then download).

Run the following command:

python -m jcvi.graphics.grabseeds seeds test.JPG

This command generates a PDF file for debugging purposes while all the identified objects will be written to stdout. If no error messages appear, congratulations! Now feel free to explore GRABSEEDS.