I was recently asked if I could provide a QIIME analysis pipeline for 16S data in Galaxy using tools in the QIIME pipeline (http://qiime.org/).

I did a bit of looking around for existing Galaxy wrappers and found an application that generates the wrappers for QIIME scripts for Galaxy (https://github.com/qiime/qiime-galaxy). This is a very well written application that does a great job of wrapping the QIIME scripts for Galaxy. However, there are a few things about it that don't quite fit my needs.


1. The tools output tgz files of all of the output files. This means that to execute a pipeline, the user would have to download the tgz files, untar, and then upload whichever file(s) are needed for the next step. 2. There is no toolshed repository to install the dependencies for these tools, making it a tricky for administrators to automate and also maintain various versions of QIIME going forward. 3. There are no toolshed versions of the tools themselves, which also makes installation and integration a bit tricky and makes it hard to me to create and manage updates, fixes, tweaks, etc. There are also no tests, etc.

For these reasons I decided to investigate the feasibility of using the generated wrappers as a basis for a "toolshed" version of QIIME. If anyone is interested in helping, or has suggestions, or is working on something related, I'd be very happy to collaborate.

The repository for the WIP is at https://github.com/lparsons/galaxy_tools/tree/qiime/tools/qiime1.9.0. There is also a package on the testtoolshed as well as a first pass at package_qiime_1_9_1 (https://github.com/lparsons/galaxy_tools/tree/qiime/packages/package_qiime_1_9_1).

--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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