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,