Re: [galaxy-dev] Trimmomatic doesn't recognise pair collection

2016-02-04 Thread 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 
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 peter.bri...@manchester.ac.uk
> 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/

Re: [galaxy-dev] Trimmomatic doesn't recognise pair collection

2016-02-04 Thread 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 > 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 peter.bri...@manchester.ac.uk

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 peter.bri...@manchester.ac.uk
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/

[galaxy-dev] Trimmomatic doesn't recognise pair collection

2016-01-22 Thread 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
___
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/