Great news, very glad this worked. I'll add liftOver to our wiki with more specific instructions and add in the bit about explicit paths to the .loc file section as well. Should help others going forward.

Thanks for taking the time to report back the solution to the list!

Jen
Galaxy team

On 7/5/12 1:47 AM, Kwon SoonJae wrote:
Hi Jen!

Definitely didn't forget to reset the server everytime I tried. The
problem was solved when I fixed the relative path to the full path..
can't believe I was stuck forever because of such a small miss. Fixed!
and everything working so far =)

Thank you so much,

SJ

On Thu, Jul 5, 2012 at 4:43 PM, Jennifer Jackson <j...@bx.psu.edu
<mailto:j...@bx.psu.edu>> wrote:

    Hello Kwon,

    There are no known issues with the liftOver wrapper (tools / extract
    / liftOver_wrapper.py and liftOver_wrapper.xml).

    Three more troubleshooting ideas:

    1 - This may sound simple, but have you restarted the database since
    you updated the .loc files?
    http://wiki.g2.bx.psu.edu/Admin/Data%20Integration (final step)

    2 - Remove the relative path from the .loc file entries (the "~/"))
    and replace with an explicit full path. I personally have not seen
    this used before in .loc files. Perhaps others on the list can
    comment about whether they have been able to use this successfully
    and if any special configuration was necessary.

    3- Confirm that the genomes are in your builds list (also covered in
    wiki above). Note that UCSC "dbkey" values have special
    capitalization rules depending on where they are used. Your example
    .loc file has this correct, but I recommend that you also check your
    builds list entries against the wiki examples and your actual data.
    If you make any changes, be sure to restart before testing.

    For example, the liftOver file pair: hg19ToDanRer6.over.chain &
    danRer6ToHg19.over.chain
    human dbkey = hg19
    zebrafish dbkey = danRer6

    Please let us know how this works out,

    Jen
    Galaxy team


    On 7/4/12 7:35 PM, Kwon SoonJae wrote:
    Hi Jen,

    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: http://pastebin.com/xSKGvUtG

    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.

    I have a feeling the error has to do with the issue with Galaxy's
    job runner returning anything written to stderr as an error,
    mentioned here:
    http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr

    Seems like it was an issue back in 2010. Has this been rectified?

    Again, thank you for your help,

    SJ

    On Wed, Jul 4, 2012 at 9:42 PM, Jennifer Jackson <j...@bx.psu.edu
    <mailto:j...@bx.psu.edu>> wrote:

        Hello Kwon,

        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).

        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).

        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).

        Thanks!

        Jen
        Galaxy team


        On 7/3/12 10:21 PM, Kwon SoonJae wrote:
        Hi Everyone,

        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't work in galaxy. Here's what I've
        done so far:

        - Downloaded liftover standalone executable from the
        tool-dependencies page in the Gwiki.

        - Changed permissions on liftover executable to make it
        usable in the command prompt (terminal, macosx) -> otherwise
        I get permission denied.

        - Copied executable over to /usr/local/bin likewise to use in
        command prompt and in Galaxy.

        - 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).

        After that I tried to run liftover in Galaxy and it didn't
        work, giving me some error that said hg19ToMm9 mapping is
        currently not available. It seems to work fine using the
        command line though.

        Since my goal is to setup galaxy locally, I really want to
        get this working correctly. Can anyone guide me through
        what's gone wrong?
        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'm
        convinced there has to be a better way.

        Thanks in advance,

        SJ


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Jennifer Jackson
http://galaxyproject.org
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