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Bwa Wrapper Local Galaxy Instance

Hi there,

I am trying to install and configure a local galaxy server for our research team. I have set up a Virtual Ubuntu 11.10 played by VirtualBox and installed galaxy using this tutorial. It amazes me that I cannot find the option to do BWA-alignment for short Illumina reads. According to the wiki there should be $GALAXY_PATH/tools/sr_mapping/bwa_wrapper.xml and $GALAXY_PATH/tool-data/bwa_index.loc which are both not present. Furthmore, when I look in the $GALAXY_PATH/tool_conf.xml in the section "NGS: Mapping" there is no record of <tool file="sr_mapping/bwa_wrapper.xml"/>

Where can I find a bwa_wrapper.xml and bwa_wrapper.py so that I can use it in my local galaxy server?

P.S. I have bwa-binary and bwa-indexed genome available so thats not an issue

galaxy
• 4,612 views • link
written by Irsan Irsan

can you please add this as an answer. Thanks.

• 0 views • link
written by Istvan Albert Istvan Albert

Hmm, but then I am answering my own question... But OK

• 81 views • link
written by Irsan Irsan

we try to encourage people to follow up and add the answers even if they get them from other sources. thanks!

• 90 views • link
written by Istvan Albert Istvan Albert

1 answer

Oops, just found it myself:

https://bitbucket.org/galaxy/galaxy-dist/src/da9d740fce31/tools/sr_mapping

• 143 views • link
written by Irsan Irsan

hey!!!

I know its maybe a little bit late but I've got a big problem which is like your one.

I made the same first steps. BWA is also installed, Version 0.7.4 and linked to the usr/local/bin folder bwa can be run from the command line:... but in "tool-data" have to be some files like bwa_index.loc.sample, but there aren't!!!

And I dont know why... I could not find the reason! :////

• 0 views • link
updated by Ram Ram • written by bubu1991anna • bubu1991anna

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