Hi Lance,

I looked at this a bit ago and had similar concerns, particularly with the 
outputs and inputs not being well-defined. In addition to the output tar ball 
—> local, extract —> upload not being great, as you mention, the input 
datatypes, etc, could use some work — in the very least, we should definitely 
create a nice biom datatype and have some converters available (import and 
export).  

Definitely worth spending some extra time to make sure that we have the data 
flowing well between each of the different parts/tools, and even better to make 
sure that its done in a way that allows mixing and matching with other 
non-qiime tools.


One thing that we want to avoid is large amounts of manual massaging of the 
automatically generated xml; fixing things up once might not be too bad, but 
having to do it with each new tool version can be “frustrating". Although 
perhaps having a good starting point and only needing to manually modify for 
any updates could be good enough (I’m not very familiar with the extent of 
typical changes between qiime versions to make a call on how much changes).




Dan

(resending since I received a message bounce from list)


On Oct 6, 2015, at 9:59 AM, Daniel Blankenberg <d...@bx.psu.edu> wrote:

> Hi Lance,
> 
> I looked at this a bit ago and had similar concerns, particularly with the 
> outputs and inputs not being well-defined. In addition to the output tar ball 
> —> local, extract —> upload not being great, as you mention, the input 
> datatypes, etc, could use some work — in the very least, we should definitely 
> create a nice biom datatype and have some converters available (import and 
> export).  
> 
> Definitely worth spending some extra time to make sure that we have the data 
> flowing well between each of the different parts/tools, and even better to 
> make sure that its done in a way that allows mixing and matching with other 
> non-qiime tools.
> 
> 
> One thing that we want to avoid is large amounts of manual massaging of the 
> automatically generated xml; fixing things up once might not be too bad, but 
> having to do it with each new tool version can be “frustrating". Although 
> perhaps having a good starting point and only needing to manually modify for 
> any updates could be good enough (I’m not very familiar with the extent of 
> typical changes between qiime versions to make a call on how much changes).
> 
> 
> 
> 
> Dan
> 
> 
> On Oct 5, 2015, at 5:26 PM, Lance Parsons <lpars...@princeton.edu> wrote:
> 
>> 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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