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,

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,


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

    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).


    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
    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,


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