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 <hrh@fmi.ch <mailto:hrh@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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