Trimmomatic doesn't recognise pair collection
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
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
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> 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/
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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 ___________________________________________________________ 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/
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
___________________________________________________________ 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.briggs@manchester.ac.uk <mailto:peter.briggs@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.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
participants (2)
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Peter Briggs -
Peter van Heusden