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).
Jen Galaxy team
On 7/3/12 10:21 PM, Kwon SoonJae wrote:
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,
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