Hello Peter

Glad that you found the problem, thanks for the update.

Best wishes

Peter

On 04/02/16 12:20, Peter van Heusden wrote:

Hi Peter

We found that it was a problem in the Galaxy code - it was fixed in the some of the patches that went towards the 16.01 release.

Thanks, Peter

On 4 February 2016 at 13:47, Peter Briggs <peter.briggs@manchester.ac.uk mailto:peter.briggs@manchester.ac.uk> wrote:

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