Hi Peter, I am wrapping https://rostlab.org/owiki/index.php/Tmseg which takes a PSSM matrix as one of the inputs so I will add the psiblast locally and test and let yo know how it goes. Thank you Eduardo On 01/02/2017 10:10, "Peter Cock" <p.j.a.cock@googlemail.com> wrote: Hi Eduardo, Certainly when Luobin Yang submitted the early work on the PSI BLAST wrapper we need the PSSM datatype to be defined, but as you note, that has been done: https://github.com/peterjc/galaxy_blast/commit/65252ee61fdd98e52454ff045fa06... According to the minimal notes I made on the issue for finishing the PSI BLAST wrapper, it is just help text and unit tests needed (which would include active user testing): https://github.com/peterjc/galaxy_blast/issues/19 If you are a PSI BLAST user, it would be very helpful to have your input here. Right now the wrapper is on the TravisCI blacklist because it would fail testing. Likewise it is not included in the Tool Shed. Peter On Wed, Feb 1, 2017 at 9:47 AM, De paiva Alves, Eduardo <eduardoalves@abdn.ac.uk> wrote: Peter I noticed there is now a PSSM datatype which is used by NCBI BLAST+ makeprofiledb. Does that allow you to remove psiblast from blacklist in your repository? https://github.com/peterjc/galaxy_blast/blob/13d5b6deca0663d7f1301428574720 b19aea1380/.tt_blacklist Thank you Eduardo On Tue, Feb 5, 2013 at 4:28 PM, Peter Cock <[hidden email]> wrote: Thanks Luobin, I've checked that into my development repository (on my tools branch): https://bitbucket.org/peterjc/galaxy-central/commits/f8f43f8494abdd228998d4 e9fe67b0f2378494e0 That will allow me to track changes etc as we work on the datatypes. Note I am not yet including ncbi_psiblast_wrapper.xml on the Galaxy Tool Shed. Regards, Peter The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683
Thank you, Peter On Wed, Feb 1, 2017 at 3:11 PM, Eduardo de Paiva Alves <alves.eduardo@gmail.com> wrote:
Hi Peter,
I am wrapping https://rostlab.org/owiki/index.php/Tmseg which takes a PSSM matrix as one of the inputs so I will add the psiblast locally and test and let yo know how it goes.
Thank you
Eduardo
On 01/02/2017 10:10, "Peter Cock" <p.j.a.cock@googlemail.com> wrote:
Hi Eduardo,
Certainly when Luobin Yang submitted the early work on the PSI BLAST wrapper we need the PSSM datatype to be defined, but as you note, that has been done:
https://github.com/peterjc/galaxy_blast/commit/65252ee61fdd98e52454ff045fa06...
According to the minimal notes I made on the issue for finishing the PSI BLAST wrapper, it is just help text and unit tests needed (which would include active user testing):
https://github.com/peterjc/galaxy_blast/issues/19
If you are a PSI BLAST user, it would be very helpful to have your input here.
Right now the wrapper is on the TravisCI blacklist because it would fail testing. Likewise it is not included in the Tool Shed.
Peter
On Wed, Feb 1, 2017 at 9:47 AM, De paiva Alves, Eduardo <eduardoalves@abdn.ac.uk> wrote: Peter
I noticed there is now a PSSM datatype which is used by NCBI BLAST+ makeprofiledb. Does that allow you to remove psiblast from blacklist in your repository?
https://github.com/peterjc/galaxy_blast/blob/13d5b6deca0663d7f1301428574720 b19aea1380/.tt_blacklist
Thank you
Eduardo
On Tue, Feb 5, 2013 at 4:28 PM, Peter Cock <[hidden email]> wrote: Thanks Luobin,
I've checked that into my development repository (on my tools branch): https://bitbucket.org/peterjc/galaxy-central/commits/f8f43f8494abdd228998d4 e9fe67b0f2378494e0
That will allow me to track changes etc as we work on the datatypes. Note I am not yet including ncbi_psiblast_wrapper.xml on the Galaxy Tool Shed.
Regards,
Peter
The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683 ___________________________________________________________ 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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participants (2)
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Eduardo de Paiva Alves -
Peter Cock