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> 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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