Hi Saket,
I haven't looked at this but I noticed the following advice on their web

If you want to call PANAMA directly from python, just take a look at the
PANAMA function inpanama.core.run.

Do you have a plan for representing the required incoming expression and
snp matrices in Galaxy?
AFAIK they need to be from the same subjects - so probably need some
thought to make it optimal for a biologist user....

On Tue, Jun 4, 2013 at 8:39 PM, Saket Choudhary <sake...@gmail.com> wrote:

> Thanks Ross and Peter. That worked.
> I think I will keep the Python wrapper though, gives me more control :)
> Saket
> On 3 June 2013 16:48, Ross <ross.laza...@gmail.com> wrote:
>> Hi Saket
>> If you want to redirect the executable's stdout to a new Galaxy dataset
>> you've defined as $output, something like:
>> &gt; '$output'
>> is a workable idiom for a command line AFAIK - you need to escape the
>> redirection '>' character or you'll confuse the xml parser.
>> It's often possible to hack a complex command line (or use configfile to
>> write a script!) but as Peter says, it all boils down to personal
>> preference - they all work.
>> Use whatever you find most convenient but remember you may need to
>> maintain it :)
>> On Mon, Jun 3, 2013 at 9:05 PM, Peter Cock <p.j.a.c...@googlemail.com>wrote:
>>> On Mon, Jun 3, 2013 at 11:53 AM, Saket Choudhary <sake...@gmail.com>
>>> wrote:
>>> > As part of a warmup, I added a tool for perming eQTL analysis using
>>> > PANAMA(http://ml.sheffield.ac.uk/qtl/panama/).
>>> >
>>> >
>>> > By default PANAMA writes to stderr and creates a PANAM_results.csv
>>> file in
>>> > the same directory as the input files.
>>> >
>>> > I wrote ... XML : https://gist.github.com/saketkc/5697388
>>> >
>>> > Apparently the above XML runs too, but I dont get back a CSV.
>>> Essentially I
>>> > need to move the PANAMA_results.csv file to output1. Can this be done
>>> > without using a  wrapper at all , just using the XML files ?
>>> >
>>> > Is there a way to nest the commands in the XML so that I could do a
>>> > <move command> after <panama command> , but how would the paths be
>>> specified
>>> > ?
>>> Hi Saket,
>>> You could try this (two commands in one shell line), but catching error
>>> conditions would be a problem:
>>> <command>panama $expression_data $snp_data; mv PANAMA_results.csv
>>> $output1</command>
>>> In cases like this where the underlying tool is too inflexible to accept
>>> an
>>> output filename, I would personally use a wrapper script which can handle
>>> moving things to the desired location, and raising a clear error if the
>>> file
>>> was not created.
>>> Peter

Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
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