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
• Pillow
• 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 Pillow jcvi

Optional: If you experience 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!