fix for GATK2 wrapper from IUC

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fix for GATK2 wrapper from IUC

Geert Vandeweyer-4
Hi,

There is a missing parameter in the unified genotyer config from the iuc
gatk2 wrapper:
The following line should be added around line 204 (just before
</expand></inputs>):

     <param name="sample_ploidy" type="integer" value="2" label="Sample
Ploidy (number of allles). For tumour, set to 2x the number of expected
subclones" help="-ploidy,--sample_ploidy" />

Without this line, activating the advanced analysis options causes the
job preparation to fail because there is a reference to it in the
<command> section


gatk2 wrapper used:
version : 8bcc13094767
hg tip:
changeset:   3:2553f84b8174
tag:         tip
user:        iuc
date:        Wed Feb 19 04:39:38 2014 -0500
summary:     Uploaded


Best,

Geert

--

Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: [hidden email]
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer

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Re: fix for GATK2 wrapper from IUC

Nicola Soranzo
Hi Geert,
thanks for the bug report, I've fixed the bug upstream:

https://github.com/bgruening/galaxytools/commit/cab6d1e84d440b7c73e99adc2bcb2c3c64c5b2c5

Björn, can you release an update on the Tool Shed? I think we have
accumulated a lot of fixes for GATK2 wrappers already.

Nicola

Il 2014-06-27 10:15 Geert Vandeweyer ha scritto:

> Hi,
>
> There is a missing parameter in the unified genotyer config from the
> iuc gatk2 wrapper:
> The following line should be added around line 204 (just before
> </expand></inputs>):
>
>     <param name="sample_ploidy" type="integer" value="2"
> label="Sample Ploidy (number of allles). For tumour, set to 2x the
> number of expected subclones" help="-ploidy,--sample_ploidy" />
>
> Without this line, activating the advanced analysis options causes
> the job preparation to fail because there is a reference to it in the
> <command> section
>
>
> gatk2 wrapper used:
> version : 8bcc13094767
> hg tip:
> changeset:   3:2553f84b8174
> tag:         tip
> user:        iuc
> date:        Wed Feb 19 04:39:38 2014 -0500
> summary:     Uploaded
>
>
> Best,
>
> Geert
>
> --
>
> Geert Vandeweyer, Ph.D.
> Department of Medical Genetics
> University of Antwerp
> Prins Boudewijnlaan 43
> 2650 Edegem
> Belgium
> Tel: +32 (0)3 275 97 56
> E-mail: [hidden email]
> http://ua.ac.be/cognitivegenetics
> http://www.linkedin.com/in/geertvandeweyer
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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