Peter,
I'm in a hurry ... have a look at
https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse
Developed by IUC member Eric Rasche.
Cheers,
Bjoern
On 18.06.2015 10:00, Peter van Heusden wrote:
I've tried that - I've added the Environment Modules for the relevant
tools to the local_env.sh file, so they're there in the environment
when Galaxy runs. These tools are scheduled via our cluster, however,
so I don't think the environment passes across to them. They depend on
these Galaxy packages, however, and those (bedtools and ucsc-utils)
are now installed, so I'm not sure why it can't pick them up from the
shed_tools.
On 18 June 2015 at 09:10, Hans-Rudolf Hotz <h...@fmi.ch
<mailto:h...@fmi.ch>> wrote:
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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