On 06/18/2015 09:06 AM, Peter van Heusden wrote:
Hi there

I'm trying to visualise some of our genome data using Trackster. Initial
input is 790,000 lines of GFF3. When I try and create the visualisation,
I get errors from two tools:

Convert GFF to Interval Index on data 3
-- an out of memory error  - I'll try and fix this by upping the memory
limit for our Galaxy jobs

Convert BED, GFF, or VCF to BigWig on data 3
-- bedtools and bedGraphToBigWig not found errors. I tried to resolve
these by installing the ucsc-tools and bedtools packages - and they did
install correctly - but I still get these file not found errors.


Hi Peter

make sure 'galaxy' (ie the user galaxy is running as) has the newly installed tools in its path. You might need to add them to "run.sh" and restart the server.


Hans-Rudolf


Any idea how to fix this second problem?

Thanks!
Peter
P.S. as an alternative to Trackster, does anyone have Galaxy interfaced
to JBrowse?


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