Bowtie for SOLiD is actually enabled as much as Bowtie for Illumina is (both are in the tool_conf.xml.sample file and both rely on the same Python file, bowtie_wrapper.py). If the tool is not loading, the most common cause is that the loc file (bowtie_indices_color.loc, which is different from the one for the Illumina version) isn't in place. If the loc file is there, then something else is wrong--check the traceback in the paster.log to see why it wouldn't load, and let us know if you have trouble fixing it. The NGSLocalSetup wiki page does address the two different loc files under the Bowtie section, though it does discuss them together because they are so similar (I also just added a column in the table showing the tool with its associated loc files to include the XML name).

On Aug 20, 2010, at 4:09 AM, Kevin Lam wrote:

Hi Kelly,
Apologies for the mispost.
I do understand the dependencies and why you cannot distribute bowtie together with galaxy.
I have bowtie on my system.
and I saw that
Map with Bowtie for Illumina
is implemented by default.
So I do not understand why
Map with Bowtie for SOLiD
isn't, since it (I presume) has the same underlying dependencies?

I am reading http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup
and
http://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial

But there's no relevant instructions on how to implement bowtie-color. Am I looking in the wrong place?

Thanks
Kevin

On Fri, Aug 20, 2010 at 1:32 PM, Kelly Vincent <kpvincent@bx.psu.edu> wrote:

Kevin,

Some of the tools in Galaxy are wrappers of external tools, and Bowtie is one such example. These underlying tools must be installed in addition to the standard Galaxy distribution, and then some extra configuration and data preparation is necessary, before the Galaxy tool can be used. There is a wiki page dedicated to installing the NGS tools (http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup) which details how to set these up. Let us know if you need further information.

(Note that this topic is better suited to galaxy-dev instead of galaxy-user since it's about local installations.)

Regards,
Kelly
Galaxy Team

On Aug 20, 2010, at 12:08 AM, Kevin Lam wrote:

Hi,
I see that the public galaxy at usegalaxy.org
has a few differences with a local installation in that some tools are not implemented as well.
for e.g.
./tools/sr_mapping/bowtie_color_wrapper.xml

May I know if there's a reason for this?

Cheers
Kevin
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