Trimmomatic wrapper for Galaxy
Hi Simon, I was looking for a Trimmomatic wrapper for Galaxy (which I have thus far only used at the command line outside of Galaxy), and while there does not seem to be one in the main Tool Shed, I see you have been working on this over on the Test Tool Shed: https://testtoolshed.g2.bx.psu.edu/view/simon-gladman/trimmomatic_0_22 https://testtoolshed.g2.bx.psu.edu/view/simon-gladman/trimmomatic_032 Note that according to http://www.usadellab.org/cms/?page=trimmomatic the Trimmomatic authors have been given permission to redistribute the Illumina adapter sequences now :) It would be nice to have functional tests, but other than that, what status is the wrapper? Are there some issues blocking releasing this via the main Tool Shed for wider use? Thanks, Peter
Hello all, I've not heard back from Simon yet (it was the weekend), but in the meantime there is a new alternative wrapper from Peter Briggs which has skipped the Test Tool Shed and gone straight to the main Tool Shed: https://toolshed.g2.bx.psu.edu/view/pjbriggs/trimmomatic This one knows Trimmomatic now bundles the Illumina adatpers, and has tests too (fingers crossed the Tool Shed tests work tonight) :) @PeterB - My only immediate feedback on scanning the repository is to try renaming README.markdown to README.md as currently the Tool Shed has not spotted and shown the README file. Regards PeterC On Fri, Nov 28, 2014 at 2:31 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Simon,
I was looking for a Trimmomatic wrapper for Galaxy (which I have thus far only used at the command line outside of Galaxy), and while there does not seem to be one in the main Tool Shed, I see you have been working on this over on the Test Tool Shed:
https://testtoolshed.g2.bx.psu.edu/view/simon-gladman/trimmomatic_0_22 https://testtoolshed.g2.bx.psu.edu/view/simon-gladman/trimmomatic_032
Note that according to http://www.usadellab.org/cms/?page=trimmomatic the Trimmomatic authors have been given permission to redistribute the Illumina adapter sequences now :)
It would be nice to have functional tests, but other than that, what status is the wrapper? Are there some issues blocking releasing this via the main Tool Shed for wider use?
Thanks,
Peter
Simon and I worked on https://testtoolshed.g2.bx.psu.edu/view/simon-gladman/ trimmomatic_032 during the BOSC 2014 Codefest to add compatibility for sets of pairs of input files via the then-new dataset collections feature. I'm not seeing support for that in Peter Briggs version though I am no expert and happy to be corrected. Hopefully the two will be merged so we don't lose the enhancements that both bring. On Mon Dec 01 2014 at 10:52:03 AM Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hello all,
I've not heard back from Simon yet (it was the weekend), but in the meantime there is a new alternative wrapper from Peter Briggs which has skipped the Test Tool Shed and gone straight to the main Tool Shed:
https://toolshed.g2.bx.psu.edu/view/pjbriggs/trimmomatic
This one knows Trimmomatic now bundles the Illumina adatpers, and has tests too (fingers crossed the Tool Shed tests work tonight) :)
@PeterB - My only immediate feedback on scanning the repository is to try renaming README.markdown to README.md as currently the Tool Shed has not spotted and shown the README file.
Regards
PeterC
On Fri, Nov 28, 2014 at 2:31 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Simon,
I was looking for a Trimmomatic wrapper for Galaxy (which I have thus far only used at the command line outside of Galaxy), and while there does not seem to be one in the main Tool Shed, I see you have been working on this over on the Test Tool Shed:
https://testtoolshed.g2.bx.psu.edu/view/simon-gladman/trimmomatic_0_22 https://testtoolshed.g2.bx.psu.edu/view/simon-gladman/trimmomatic_032
Note that according to http://www.usadellab.org/cms/?page=trimmomatic the Trimmomatic authors have been given permission to redistribute the Illumina adapter sequences now :)
It would be nice to have functional tests, but other than that, what status is the wrapper? Are there some issues blocking releasing this via the main Tool Shed for wider use?
Thanks,
Peter
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participants (2)
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Michael R. Crusoe -
Peter Cock