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
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
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
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
There is also a package on the testtoolshed as well as a first pass at
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
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