Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

[Floreline TOUCHARD]

Hi,

sorry for the late response ! I tested the modifications proposed in the "Allow
to select multiple database" pull request and it works !!!

Thanks a lot !
Floreline.

P.S : I'm not familiar with all github functionnalities yet, but I will
work on it ;)

2016-01-20 16:07 GMT+01:00 Peter Cock :

> On Wed, Jan 20, 2016 at 2:43 PM, Gildas Le Corguillé
>  wrote:
> > Hi,
> >
> > A long time ago, in a far far svn repo, we did this "multiple=true" on
> Peter
> > wrappers.
> >
> > I will try to propose it quickly :)
> >
> > Gildas
>
> Great - a pull request against https://github.com/peterjc/galaxy_blast
> but if your SVN repo is still online, or you can make a patch/diff file,
> we could look at that and try to port the changes. My guess is a lot
> of macro work was done in the meantime so it may not be trivial to
> repeat your changes :(
>
> Thanks,
>
> Peter
>
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Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

[Peter Cock]

Good to know :)

https://github.com/peterjc/galaxy_blast/pull/77

The pull request looks good - sadly distracted by TravisCI
failures from Galaxy/planemo/dependency changes.

Thanks,

Peter

On Tue, Feb 9, 2016 at 3:28 PM, Floreline TOUCHARD
 wrote:
> Hi,
>
> sorry for the late response ! I tested the modifications proposed in the
> "Allow to select multiple database" pull request and it works !!!
>
> Thanks a lot !
> Floreline.
>
> P.S : I'm not familiar with all github functionnalities yet, but I will work
> on it ;)
>
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Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

[Peter Cock]

On Wed, Jan 20, 2016 at 2:43 PM, Gildas Le Corguillé
 wrote:
> Hi,
>
> A long time ago, in a far far svn repo, we did this "multiple=true" on Peter
> wrappers.
>
> I will try to propose it quickly :)
>
> Gildas

Great - a pull request against https://github.com/peterjc/galaxy_blast
but if your SVN repo is still online, or you can make a patch/diff file,
we could look at that and try to port the changes. My guess is a lot
of macro work was done in the meantime so it may not be trivial to
repeat your changes :(

Thanks,

Peter
___
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Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

[Peter Cock]

On Wed, Jan 20, 2016 at 9:19 AM, Floreline TOUCHARD
 wrote:
> Hi,
>
> I would like to add some tools of the EMBOSS suite (6.6.0) to my Galaxy
> instance. It seems that the only wrapper available for Galaxy is for the
> 5.0.0 version
> (http://dev.list.galaxyproject.org/Galaxy-with-EMBOSS-5-or-EMBOSS-6-td4658043.html).
>
> I would like to know if someone has already tried (successfully or not) to
> wrap this tools base on the old wrappers to estimate the workload that
> awaits me (for prettyseq and water mostly).

There is work in progress here, see:
https://github.com/galaxyproject/tools-iuc/issues/65
https://github.com/galaxyproject/tools-iuc/pull/131

Have you compared the API options to see if anything changed
here in EMBOSS? I don't recall any major changes to water,
but I don't use prettyseq at all.

> Could there be an invalid datatype format for example ?

Many datatypes were already defined for the EMBOSS 5.0.0
wrappers, so that is less likely to be a problem for EMBOSS 6.6.0

> I have another question regarding the NCBI BLAST+ suite : is there a way to
> edit the XML file to enable the selection of multiple databases as proposed
> by the command lines tool ?

Possible by editing the wrappers, yes. However it will likely break
if any of the paths have spaces in them due to the NCBI wanting
a space separated list of database paths - a potential problem
already in the makeblastdb wrapper.

Are you wanting to use multiple databases from the *.loc files at
once, multiple databases from the current history, or both? Please
log this as an enhancement request here:

https://github.com/peterjc/galaxy_blast/issues

Thanks,

Peter
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Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

[Peter Cock]

On Wed, Jan 20, 2016 at 2:22 PM, Floreline TOUCHARD
 wrote:
> Thanks for the answer !
>
> I compared the two versions of tools. It does not seem to be any major
> differences indeed. I added these tools to my instance successfully.

Great :)

> Additional options in version 6 are not to be integrate to my Galaxy
> instance immediately. I will update my XML file later if need arises. The
> old wrappers are perfect for the moment.

If you have any feedback on the IUC work, please comment on the
GitHub issue.

> For the NCBI BLAST+ suite I would like to select multiple databases only
> from the *.loc files. There is no spaces in the paths in my *.loc files
> (however there is spaces in the names of these databases, but I guess this
> is not a problem). I thought I just have to add a tag "multiple=true" in the
> XML file but it seems a bit more complex. Am I missing something ?

As far as I know, the multiple="true" tag only works on input datasets
from your history. But that would make sense... I don't think I have
ever tried this.

Even if that worked, the  tag would also need modifying
to account for the multiple values from db_opts.database.

Another potential option is to extend makeblastdb which can in
principle combine multiple FASTA and pre-existing databases...

Peter
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Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

[Gildas Le Corguillé]

Hi,

A long time ago, in a far far svn repo, we did this "multiple=true" on Peter 
wrappers.

I will try to propose it quickly :)

Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
http://abims.sb-roscoff.fr
--



> Le 20 janv. 2016 à 15:37, Peter Cock  a écrit :
> 
> On Wed, Jan 20, 2016 at 2:22 PM, Floreline TOUCHARD
>  wrote:
>> Thanks for the answer !
>> 
>> I compared the two versions of tools. It does not seem to be any major
>> differences indeed. I added these tools to my instance successfully.
> 
> Great :)
> 
>> Additional options in version 6 are not to be integrate to my Galaxy
>> instance immediately. I will update my XML file later if need arises. The
>> old wrappers are perfect for the moment.
> 
> If you have any feedback on the IUC work, please comment on the
> GitHub issue.
> 
>> For the NCBI BLAST+ suite I would like to select multiple databases only
>> from the *.loc files. There is no spaces in the paths in my *.loc files
>> (however there is spaces in the names of these databases, but I guess this
>> is not a problem). I thought I just have to add a tag "multiple=true" in the
>> XML file but it seems a bit more complex. Am I missing something ?
> 
> As far as I know, the multiple="true" tag only works on input datasets
> from your history. But that would make sense... I don't think I have
> ever tried this.
> 
> Even if that worked, the  tag would also need modifying
> to account for the multiple values from db_opts.database.
> 
> Another potential option is to extend makeblastdb which can in
> principle combine multiple FASTA and pre-existing databases...
> 
> Peter
> ___
> Please keep all replies on the list by using "reply all"
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Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

[Floreline TOUCHARD]

Thanks for the answer !

I compared the two versions of tools. It does not seem to be any major
differences indeed. I added these tools to my instance successfully.
Additional options in version 6 are not to be integrate to my Galaxy
instance immediately. I will update my XML file later if need arises. The
old wrappers are perfect for the moment.

For the NCBI BLAST+ suite I would like to select multiple databases
only from the *.loc files. There is no spaces in the paths in my *.loc
files (however there is spaces in the names of these databases, but I guess
this is not a problem). I thought I just have to add a tag "multiple=true"
in the XML file but it seems a bit more complex. Am I missing something ?

F.T


2016-01-20 10:33 GMT+01:00 Peter Cock :

> On Wed, Jan 20, 2016 at 9:19 AM, Floreline TOUCHARD
>  wrote:
> > Hi,
> >
> > I would like to add some tools of the EMBOSS suite (6.6.0) to my Galaxy
> > instance. It seems that the only wrapper available for Galaxy is for the
> > 5.0.0 version
> > (
> http://dev.list.galaxyproject.org/Galaxy-with-EMBOSS-5-or-EMBOSS-6-td4658043.html
> ).
> >
> > I would like to know if someone has already tried (successfully or not)
> to
> > wrap this tools base on the old wrappers to estimate the workload that
> > awaits me (for prettyseq and water mostly).
>
> There is work in progress here, see:
> https://github.com/galaxyproject/tools-iuc/issues/65
> https://github.com/galaxyproject/tools-iuc/pull/131
>
> Have you compared the API options to see if anything changed
> here in EMBOSS? I don't recall any major changes to water,
> but I don't use prettyseq at all.
>
> > Could there be an invalid datatype format for example ?
>
> Many datatypes were already defined for the EMBOSS 5.0.0
> wrappers, so that is less likely to be a problem for EMBOSS 6.6.0
>
> > I have another question regarding the NCBI BLAST+ suite : is there a way
> to
> > edit the XML file to enable the selection of multiple databases as
> proposed
> > by the command lines tool ?
>
> Possible by editing the wrappers, yes. However it will likely break
> if any of the paths have spaces in them due to the NCBI wanting
> a space separated list of database paths - a potential problem
> already in the makeblastdb wrapper.
>
> Are you wanting to use multiple databases from the *.loc files at
> once, multiple databases from the current history, or both? Please
> log this as an enhancement request here:
>
> https://github.com/peterjc/galaxy_blast/issues
>
> Thanks,
>
> Peter
>
___
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