Hi Peter,
Thanks for you quick answer! But I am very new to Galaxy. Could you explain 
something about those symlinks?

From: Peter Cock [p.j.a.c...@googlemail.com]
Sent: Wednesday, June 20, 2012 4:01 PM
To: Heijden, J.W.F. van der (HG)
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] samtools view region

On Wed, Jun 20, 2012 at 2:59 PM,  <j.w.f.van_der_heij...@lumc.nl> wrote:
> Hi all,
> I was working on the integration of the "samtools view" to work with Galaxy.
> The idea is to filter an indexed bam file on a chromosome with "samtools
> view -bh in.bam.bai chr1".
> After some research I noted that samtools will only execute this command
> when it can find the corresponding sorted bam file, so the "in.bam".
> The problem is that Galaxy renames all the files. So "in.bam" will be for
> instance dataset_1.dat. When I index the bam file I will get an indexed bam
> file named dataset_2.dat. Samtools can't detect then that dataset_1.dat is
> the sorted bam file and dataset_2.dat is the bai file.
> Now I was wondering if it is possible to rename files in the
> ~/galaxy-dist/database/files/000 with a command line. So that dataset_2.dat
> will be moved to dataset_1.dat.bai.
> Does anyone know how to do that?
> Kind Regards,
> Jaap

The simple answer is a wrapper script which makes symlinks for
the BAM file and its BAI file using the normal naming conventions.


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