Hi Jen,<div><br></div><div>Thanks for looking into this. I have unzipped all the .gz files so that the directory contains all .chain files. The liftover.loc file has also been modified to refer to all the .chain files instead, as such: <a href="http://pastebin.com/xSKGvUtG">http://pastebin.com/xSKGvUtG</a></div>
<div><br></div><div>I still run into the same error if I try to run the tool in Galaxy, though (hg19ToMm9 mapping currently not available). The liftover command still works fine through the command line.</div><div><br></div>
<div>I have a feeling the error has to do with the issue with Galaxy&#39;s job runner returning anything written to stderr as an error, mentioned here: <a href="http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr">http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr</a></div>
<div><br></div><div>Seems like it was an issue back in 2010. Has this been rectified?</div><div><br></div><div>Again, thank you for your help,</div><div><br></div><div>SJ</div><div><br><div class="gmail_quote">On Wed, Jul 4, 2012 at 9:42 PM, Jennifer Jackson <span dir="ltr">&lt;<a href="mailto:jen@bx.psu.edu" target="_blank">jen@bx.psu.edu</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
  
    
  
  <div text="#000000" bgcolor="#FFFFFF">
    Hello Kwon,<br>
    <br>
    
    Most of this sounds correct. The only issue is with compressed
    files. Galaxy uses uncompressed liftOver data at our site and this
    is how we instruct that it be set up (see
    galaxy-central/tool-data/liftOver.loc.sample).<br>
    <br>
    Would you be able to run a test to see if uncompressing resolves the
    issue? Uncompress one of the over.chain files, modify the .loc file
    so that the name also reflects the uncompressed naming, then try to
    use the UI version of liftOver with this uncompressed data. Please
    let us know how this works out (cc-ing the list, so that others can
    learn of the confirmed dependency).<br>
    <br>
    For now, there is no automated way to enter the .loc data entries.
    There is some development activity going on right now to address
    data setup (including liftOver), but nothing is ready yet to be
    shared. When complete, any new tools will be announced (loudly - we
    know that they are highly desired).<br>
    <br>
    Thanks!<br>
    <br>
    Jen<br>
    Galaxy team<div><div class="h5"><br>
    <br>
    <div>On 7/3/12 10:21 PM, Kwon SoonJae wrote:<br>
    </div>
    </div></div><blockquote type="cite"><div><div class="h5">
      <div>Hi Everyone,</div>
      <div><br>
      </div>
      <div>I installed a local instance of galaxy and some tools using
        the command line, and for some reason liftover will work in the
        command line but won&#39;t work in galaxy. Here&#39;s what I&#39;ve done so
        far:</div>
      <div><br>
      </div>
      <div>- Downloaded liftover standalone executable from the
        tool-dependencies page in the Gwiki.</div>
      <div><br>
      </div>
      <div>- Changed permissions on liftover executable to make it
        usable in the command prompt (terminal, macosx) -&gt; otherwise
        I get permission denied.</div>
      <div><br>
      </div>
      <div>- Copied executable over to /usr/local/bin likewise to use in
        command prompt and in Galaxy.</div>
      <div><br>
      </div>
      <div>- Modified liftover.loc to include all the conversion types
        and directories of chain.gz files I downloaded to use with the
        tool (I believe liftover can make use of both .chain and
        .chain.gz files).</div>
      <div><br>
      </div>
      <div>After that I tried to run liftover in Galaxy and it didn&#39;t
        work, giving me some error that said hg19ToMm9 mapping is
        currently not available. It seems to work fine using the command
        line though.</div>
      <div><br>
      </div>
      <div>Since my goal is to setup galaxy locally, I really want to
        get this working correctly. Can anyone guide me through what&#39;s
        gone wrong?</div>
      <div>Also, there must be a better way of installing all these
        tools than manually downloading every single one and using the
        command line, surely? I had to type out the format of
        liftover.loc file manually for around 130 chain files... I&#39;m
        convinced there has to be a better way.</div>
      <div><br>
      </div>
      <div>Thanks in advance,</div>
      <div><br>
      </div>
      <div>SJ</div>
      <br>
      <fieldset></fieldset>
      <br>
      </div></div><pre>___________________________________________________________
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    </font></span></blockquote><span class="HOEnZb"><font color="#888888">
    <br>
    <pre cols="72">-- 
Jennifer Jackson
<a href="http://galaxyproject.org" target="_blank">http://galaxyproject.org</a></pre>
    <br>
    <br>
  </font></span></div>

</blockquote></div><br></div>