[Bio-Linux] Biolinux7_Galaxy_Tophat_error

Jeremy Shearman jeremy.she at biotec.or.th
Fri Sep 6 09:52:47 EDT 2013


Hi
     Yes upgrading fixed my problem.  Try running from the terminal using the fastq file, if that works it has to be a galaxy issue.


Sent from Samsung Mobile



-------- Original message --------
From: "Miskey, Csaba" <Csaba.Miskey at pei.de>
Date: 06/09/2013 19:25 (GMT+07:00)
To: bio-linux at nebclists.nerc.ac.uk
Cc: tbooth at ceh.ac.uk,Jeremy Shearman <jeremy.she at biotec.or.th>
Subject: Biolinux7_Galaxy_Tophat_error


Dear Guys,

I wonder if Jeremy’s problem with Tophat (error when trying to run it) was solved by updating to 2.0.9.
My Galaxy running under Biolinux7 has Tophat 2.0.9. and I still cannot make it run. (Bowtie accepts and runs ok with the same fastqsanger file with which Tophat throws the error. Though, as I figured the two mappers take the same set of indexes).

Any help would be greatly appreciated!

Best wishes,

Csaba
(new in the field)


Hi Jeremy,

I've pushed the update through for Tophat so it should become available
later today.

Note that bowtie is a legacy program that is unlikely to be updated
again.  The latest bowtie2 is packaged separately in the bowtie2 package
(currently 2.1.0).

Cheers,

TIM

On Tue, 2013-08-27 at 06:44 +0100, Jeremy Shearman wrote:
> Hi Tim
>              Can you please update the bio-linux tophat version to
> v2.0.9 because the current bio-linux version (2.0.8) is not compatible
> with the current bio-linux version of bowtie (v1.0.0) and throws an
> error when you try and run tophat.
>
> Thanks
> Jeremy

Csaba Miskey Ph.D.

Paul Ehrlich Institut
Medical Biotechnology
Paul Ehrich Str. 51-59
63225 Langen, Germany

Tel: +49 06103 773407
csaba.miskey at pei.de

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