Hello Peter

I'm the author of the Trimmomatic tool on the toolshed (i.e.
https://toolshed.g2.bx.psu.edu/view/pjbriggs/trimmomatic) - apologies for not responding sooner.

The tool works for me on our production server (v15.10 from github) when using a pair of fastqs as input, by which I mean that it allows me to select a fastq-pair dataset as input and produces 2 fastq-pair datasets. (I'm haven't tried on a list of pairs.)

What do you see when you say that the tool 'is not working'? I'm wondering if it is a problem with the tool itself, or something to do with the underlying Galaxy infrastructure when using the head of the dev branch).

Best wishes

Peter

On 22/01/16 13:53, Peter van Heusden wrote:

Hi there

I've got Trimmomatic installed (from the toolshed) into our local Galaxy
server (server is latest commit on the dev branch from GitHub). It
refuses to see a dataset pair as a valid input, however.

I've tested this with two types: firstly a pair made out of 2 individual
datasets (both fastqsanger) and then also a list of pairs. I've tested
this with 'planemo serve' and the tool works, but for some reason it is
not working on our server. Any ideas?

Thanks,
Peter

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Peter Briggs peter.briggs@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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