Question: Bwa Wrapper Local Galaxy Instance
0
gravatar for Irsan
6.4 years ago by
Irsan6.8k
Amsterdam
Irsan6.8k wrote:

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 • 3.0k views
ADD COMMENTlink written 6.4 years ago by Irsan6.8k
2
gravatar for Irsan
6.4 years ago by
Irsan6.8k
Amsterdam
Irsan6.8k wrote:

Oops, just found it myself:

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

ADD COMMENTlink written 6.4 years ago by Irsan6.8k

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! :////

ADD REPLYlink written 5.0 years ago by bubu1991anna0
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