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Peter Cock <p.j.a.cock@googlemail.com>

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Peter Cock <p.j.a.cock@googlemail.com>

Eduardo de Paiva Alves
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" <[hidden email]> 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/65252ee61fdd98e52454ff045fa069f04ec40c06

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
<[hidden email]> 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
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Re: Peter Cock <p.j.a.cock@googlemail.com>

Peter Cock
Thank you,

Peter

On Wed, Feb 1, 2017 at 3:11 PM, Eduardo de Paiva Alves
<[hidden email]> 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" <[hidden email]> 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/65252ee61fdd98e52454ff045fa069f04ec40c06
>
> 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
> <[hidden email]> 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/
>
> 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/
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