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
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
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.ed
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
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 resol
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.
