November 2018
Intermediate to advanced
360 pages
9h 36m
English
Content preview from Bioinformatics with Python Cookbook - Second Edition
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Getting ready
Strictly speaking, tool development is language-agnostic. Many tools are actually just wrappers for existing applications; no Python code involved. But Python is well-suited to tool development, especially because Galaxy is implemented in Python, so it's the best choice for tool development. Planemo is actually a Python tool, so you will need Python in any case.
We are going to develop a very basic tool here: we will take a BED file, count the number of entries, and compute some basic statistics. The point here is not the tool itself, but all the artifacts needed to develop the tool.
At this stage, installing Planemo with conda is not stable. Also, Planemo is Python 2, not 3. As such, we will go back in time and use Python 2, ...