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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