Hi Ross,



On 4 June 2013 16:15, Ross <ross.laza...@gmail.com> wrote:

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

Yes, using the API makes more sense. Currently I am relying on the end user
to choose the proper set of files to run PANAMA.

AFAIK they need to be from the same subjects - so probably need some
> thought to make it optimal for a biologist user....
>
>
I think this will possibly require the user to upload the dataset with
proper naming. say :
<mydata>_expression.csv
 and <mydata>_snp.csv

Is there a way in Galaxy to restrict this kind of thing ? I am not sure
though, that forcing such constraints will make sense, this is just a
suggestion. But as you correctly pointed out, there is a need to organise
the data to ensure the correct dataset is fed to PANAMA or for that matter
the other tools I am working on.


Saket


>
>
> 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
> http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
>
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