[galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)

[Lance Parsons]

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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[galaxy-dev] External Pipeline Cleanup

[Ryan G]

Hi all - For various reasons, we've had to implement our pipelines external
to Galaxy, but still give Galaxy the ability to run them.  I've
accomplished this by having the Galaxy tool wrapper call the external app
to launch the pipelines.

My problem is that when a user aborts the tool, the tool needs to be able
to communicate to the pipeline that its need aborted.  How can I do this?
Is there some way to get a notification that the job has been cancelled
before its actually cancelled to perform clean up?
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