Hi Kelly, <br>Apologies for the mispost.<br>I do understand the dependencies and why you cannot distribute bowtie together with galaxy. <br>I have bowtie on my system. <br>and I saw that <br><a id="link-bowtie_wrapper" href="http://node03:8080/tool_runner?tool_id=bowtie_wrapper" target="galaxy_main">Map with Bowtie for Illumina</a><br>

is implemented by default. <br>So I do not understand why <br><a id="link-bowtie_color_wrapper" href="http://main.g2.bx.psu.edu/tool_runner?tool_id=bowtie_color_wrapper" target="galaxy_main">Map with Bowtie for SOLiD</a><br>

isn&#39;t, since it (I presume) has the same underlying dependencies?<br><br>I am reading <a href="http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup">http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup</a><br>

and <br><a href="http://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial">http://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial</a><br><br>But there&#39;s no relevant instructions on how to implement bowtie-color. Am I looking in the wrong place?<br>

<br>Thanks<br>Kevin<br><br><div class="gmail_quote">On Fri, Aug 20, 2010 at 1:32 PM, Kelly Vincent <span dir="ltr">&lt;<a href="mailto:kpvincent@bx.psu.edu">kpvincent@bx.psu.edu</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">

<div style=""><div>Kevin,</div><div><br></div><div>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 (<a href="http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup" target="_blank">http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup</a>) which details how to set these up. Let us know if you need further information.</div>

<div><br></div><div><div>(Note that this topic is better suited to galaxy-dev instead of galaxy-user since it&#39;s about local installations.)</div></div><div><br></div><div>Regards,</div><div>Kelly</div><div>Galaxy Team</div>

<div><br></div><div><br></div><br><div><div><div></div><div class="h5"><div>On Aug 20, 2010, at 12:08 AM, Kevin Lam wrote:</div><br></div></div><blockquote type="cite"><div><div></div><div class="h5">Hi, <br>I see that the public galaxy at <a href="http://usegalaxy.org" target="_blank">usegalaxy.org</a> <br>

has a few differences with a local installation in that some tools are not implemented as well. <br>for e.g. <br>./tools/sr_mapping/bowtie_color_wrapper.xml<br> <br>May I know if there&#39;s a reason for this?<br><br>Cheers<br>

Kevin<br></div></div> _______________________________________________<br>galaxy-user mailing list<br><a href="mailto:galaxy-user@lists.bx.psu.edu" target="_blank">galaxy-user@lists.bx.psu.edu</a><br><a href="http://lists.bx.psu.edu/listinfo/galaxy-user" target="_blank">http://lists.bx.psu.edu/listinfo/galaxy-user</a><br>

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