v3.2

Minor fixes, and updates to https://merenlab.org/2014/08/16/installing-the-oligotyping-pipeline/

v3.1

Includes a fix through #35 by Benjamin C C Hume (@didillysquat) that enables the proper decomposition of the root node if the end condition for decomposition is satisfied during the very first step of the process.

v3

Includes a switch to Python 3 and minor fixes.

Bug fixes

Various bugs are fixed. One of the major change is the use of two flags for oligotype and decompose:

• --skip-blast-search is replaced with --do-blast-serach. The previous default behavior, searching every representative sequence in nr at the end of oligotyping, was quite a bit of pain for new users. Now the pipeline will perform that step only if it is specifically asked.
• Similarly, --gen-html-output flag is now removed, and instead we have a --skip-gen-html flag. Clearly, the power of the oligotyping pipeline is the fact that it allows users to get their hands dirty with their data through the advanced HTML output it generates. Hence, skipping it is a better option than having to ask for this essential output during every run. This also affects the decompose command.

Plus, @gkmngrgn kindly fixed the template issue with newer Django versions (e0b793e).

More info on the oligotyping pipeline is here: http://merenlab.org/projects/oligotyping/

Thank you very much!

v2.0

Fixing a ancient bug: remove carriage return characters from sample m…