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Old 03-13-2014, 03:55 AM   #1
Anek
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Location: Germany

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Default Installed bwa, but there are no bwa files produced in Galaxy

Hello guys,


I've got a problem with the integration of the BWA Tool in Galaxy.
I installed BWA and Galaxy in a virtual box and now I want integrate BWA as a tool.
For this I have to do this steps:


$ sudo cp /home/ubuntu/Galaxy/BWA/bwa-0.6.2/bwa /usr/local/bin
Now bwa can be run from the command line:

$ bwa
Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.4-r385
Contact: Heng Li <lh3@sanger.ac.uk>
...

The Galaxy tool also requires a loc file which contains the locations of indexes for locally stored genome builds. We don't have any, so we can just use the empty sample:

$ cp tool-data/bwa_index.loc.sample tool-data/bwa_index.loc


$ sh run.sh --reload


The problem is, that in my tool-data folder doesn't exist bwa files even if bwa is installed and also linked in the bin folder!


Thanks and greetings
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Old 03-13-2014, 01:35 PM   #2
westerman
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Sending email to the Galaxy mailing list will probably get you a faster and more complete response. I have the feeling that many of the people on this message board do not use Galaxy or set it up.
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Old 03-13-2014, 01:57 PM   #3
GenoMax
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Did you follow the instructions on this wiki page: https://wiki.galaxyproject.org/Admin...Local%20Setup?
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Old 03-13-2014, 03:40 PM   #4
Anek
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I have sent my question to galaxy and to another discussion forum... but nobody answered me yet...


Yes I do. But I get another error message which sounds like this --> zhs: parse error near \n


I don't understand it ... I really don't know what to do!

Last edited by Anek; 03-13-2014 at 03:43 PM.
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Old 03-14-2014, 04:23 AM   #5
GenoMax
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Quote:
Originally Posted by Anek View Post
Yes I do. But I get another error message which sounds like this --> zhs: parse error near \n
Can you post a more complete listing of the error message(s)? What is the exact context for the error above?
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