Installed Bwa But There Are No Bwa Files Produced In Galaxy-Dist Folder

Question

[bubu1991anna]

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-dist/bwa-0.7.4/bwa  /usr/local/bin

now bwa can be run from the command line

$ bwa

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!

I hope you can help me, because I don't know what to do now!

Thanks and greets,
Anna

[skymningen]

You are supposed to make the .loc files yourself, so they match the sample, but include the right paths to were your BWA indices are stored. The second sentence of the header for the example file is "You will need to create these data files and then create a bwa_index.loc file similar to this one (store it in this directory) that points to the directories in which those files are stored."

Answer 1

[martenson]

The easiest way to get tools into your Galaxy is to install some existing tools via the Admin interface. There are multiple bwa tools available via the Galaxy's appstore - The Tool Shed (http://toolshed.g2.bx.psu.edu/). Try some of the bwa wrappers already present there - e.g. http://toolshed.g2.bx.psu.edu/repository?repository_id=25bdd3c7f0d57b06

EDIT: I have improved the Galaxy wiki to bring more clarity into this process. Please see https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial