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:
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
But there's no relevant instructions on how to implement bowtie-
color. Am I looking in the wrong place?
On Fri, Aug 20, 2010 at 1:32 PM, Kelly Vincent
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
(Note that this topic is better suited to galaxy-dev instead of
galaxy-user since it's about local installations.)
On Aug 20, 2010, at 12:08 AM, Kevin Lam wrote:
> 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.
> May I know if there's a reason for this?
> galaxy-user mailing list