Trimmomatic doesn't recognise pair collection

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Trimmomatic doesn't recognise pair collection

Peter van Heusden
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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Re: Trimmomatic doesn't recognise pair collection

Peter Briggs
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
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>    https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/
>

--
Peter Briggs [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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Re: Trimmomatic doesn't recognise pair collection

Peter van Heusden
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 <[hidden email]> 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


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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--
Peter Briggs [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
___________________________________________________________
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Re: Trimmomatic doesn't recognise pair collection

Peter Briggs
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 <[hidden email]
> <mailto:[hidden email]>> 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
>
>
>         ___________________________________________________________
>         Please keep all replies on the list by using "reply all"
>         in your mail client.  To manage your subscriptions to this
>         and other Galaxy lists, please use the interface at:
>         https://lists.galaxyproject.org/
>
>         To search Galaxy mailing lists use the unified search at:
>         http://galaxyproject.org/search/mailinglists/
>
>
>     --
>     Peter Briggs [hidden email]
>     <mailto:[hidden email]>
>     Bioinformatics Core Facility University of Manchester
>     B.1083 Michael Smith Bldg Tel: (0161) 2751482
>     ___________________________________________________________
>     Please keep all replies on the list by using "reply all"
>     in your mail client.  To manage your subscriptions to this
>     and other Galaxy lists, please use the interface at:
>     https://lists.galaxyproject.org/
>
>     To search Galaxy mailing lists use the unified search at:
>     http://galaxyproject.org/search/mailinglists/
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>    https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/
>

--
Peter Briggs [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/