jpuritz
commented
5 years ago Hi Rob,
Thanks for reaching out. I'm reluctant to consider this change because it won't change any functionality for dDocent, it will instantly be incompatible with previous installs/environments, and will require time for implementation and testing. It will also require time for getting users of previous versions up to speed.
As far as I know, PEAR is distributed under the creative commons license that only prohibits commercial use. See (https://cme.h-its.org/exelixis/web/software/pear/doc.html) and (http://www.exelixis-lab.org/pear). It can be installed via bioconda which is my preferred environmental management system.
That being said. PANDAseq seems like a fine package, so I'm willing to consider it if you want to submit a pull request. Even better if you can provide some testing.
Hi Jonathan,
As part of my work with the Genomics for Aotearoa New Zealand society, I am building docker containers for bioinformatics tools. It would be great to build a fully functional one for dDocent. Unfortunately, the PEAR software has two significant issues prohibiting inclusion. The first is that it is just not available in a way one can script up an install. The second is that it does not have a suitable license for software distribution.
On the other hand, PANDAseq is available from their github repo under free software licensing terms. https://github.com/neufeld/pandaseq It implements many algorithms, including the one used by PEAR. If you wouldn't mind substituting PANDAseq for PEAR, I would then be able to build a docker container of dDocent with full functionality.
Thank you for considering my request.
--Rob