[Bioperl-l] Galaxy tools?

Florent Angly florent.angly at gmail.com
Sun Nov 27 21:09:45 EST 2011

Hi Russell,

As Peter said, the tools to be wrapped do not need to be written in Python.

I have build a few wrappers for Galaxy, including one for the read 
simulator Grinder (http://sourceforge.net/projects/biogrinder/), which 
uses Bioperl and is available in the Galaxy Toolshed 
(http://sourceforge.net/projects/biogrinder/). It is not very hard to do 
a wrapper for trivial programs, but becomes more complicated once you 
start having optional arguments or multiple output files.

Grinder uses Getopt::Euclid (http://search.cpan.org/dist/Getopt-Euclid/) 
to parse command-line arguments. I have been thinking about leveraging 
the information that Getopt::Euclid stores about command-line arguments 
to automate most of the Galaxy wrapper generation, but I have not gotten 
to it yet.


On 28/11/11 11:28, Peter Cock wrote:
> On Monday, November 28, 2011, Smithies, Russell  wrote:
>> Possibly the wrong place to ask but has anyone written
>> Galaxy tools using BioPerl?
>> I was thinking of creating blast graphic and format converter
>>   tools as I couldn't see any already available in their toolbox.
>> It looks like I can just write a Python wrapper for my existing
>> BioPerl scripts - although I suspect the "correct" method is to
>> use BioPython methods (but Python annoys me with its lack
>> of semi-colons and required white-space)
> Galaxy is agnostic about what language the tools are in,
> you can use a binary, shell script, Java, Perl, Python etc.
> Peter
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