[galaxy-user] Creating a Trackster visualisation from a reference in your history

[graham etherington (TSL)]

Hi,
I’m struggling to figure out how to visualise a SAM file in Trackster as a 
normal user (i.e. without admin privileges). I’ve tried both my local install 
and use galaxy.org.
This is what I’ve done on usegalaxy.org:
Uploaded paired-end fastq sequences and a reference fasta file.
Mapped with BWA.
Clicked on SAM output – Visualize  Trackster
Chose 'View in new visualisation’, then ‘Add a Custom Build’.
In the ‘Add a Custom Build’ I give my build the name ‘solanum_reference’ and 
the key ‘solanum_reference_1’. I select the fasta mapping reference from my 
history under the ‘FASTA’ tab and under the Len File entry I upload a .len file 
(tab-delimited) called ‘solanum_reference_1.len’.
I navigate back to my SAM history item, associate the Database/Build with my 
new build (via the Edit attributes icon) and then again Visualize  Trackster  
View in New Visualization. I name the Browser, select my ‘solanum_reference’ as 
the 'Reference genome build' and hit ‘Create’.
The view changes to the Trackster Browser and at the top I reads: Preparing 
data, This can take a while for a large dataset…..etc., etc. 
After a few minutes, this changes too: “Cannot display dataset due to an 
error.” If I click on ‘View error’ I get:

Couldn't open /galaxy/data/chrom/solanum_reference_1.len , No such file or 
directory

Is it possible to create a custom build and use it to view a SAM file without 
adding the .len and .2bit files in to the Galaxy file system as an 
administrator?
If so, what am I doing wrong?

Many thanks,
Graham


Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601
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Re: [galaxy-user] Creating a Trackster visualisation from a reference in your history

[Jeremy Goecks]

 Is it possible to create a custom build and use it to view a SAM file without 
 adding the .len and .2bit files in to the Galaxy file system as an 
 administrator?

Yes, it definitely is.

 If so, what am I doing wrong?


This is a Galaxy bug which has been fixed in this commit:

https://bitbucket.org/galaxy/galaxy-central/commits/117fef56513fc563dd231516196cfd601c1635e2

We have a release coming up, so this fix will be included in the release and 
will make it to our public server soon. In the meantime, note that you can use 
the genome fasta file rather than the len file to create a custom build and 
everything should work.

Thanks,
J.

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