Re: [galaxy-dev] Blast db permission

2017-02-22 Thread SAPET, Frederic 
Hello,

I have also the same needs !

Would it be possible to enable Cheetah conditionnals within the  tag ?

Something like this :

#if ($__user_email__.endswith('biogemma.com'))



#else



#end if


Fred

De : galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] De la part 
de Gildas Le Corguillé
Envoyé : vendredi 20 janvier 2017 10:22
À : Peter Cock <p.j.a.c...@googlemail.com>
Cc : Galaxy Dev List <galaxy-dev@lists.galaxyproject.org>
Objet : Re: [galaxy-dev] Blast db permission

Hello Mohamed,

Two years ago, we had exactly the same needs (actually, we still have) and took 
an internship to investigate and develop a solution to privatize blast databank 
through Galaxy.
As many projects, we didn’t find enough time to finalize that.

I have just push the different scripts we have if you want to test or just have 
a look: https://github.com/abims-sbr/galaxy-blastprivate

Cheers

Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org<http://workflow4metabolomics.org/>

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
--


Le 19 janv. 2017 à 14:53, Peter Cock 
<p.j.a.c...@googlemail.com<mailto:p.j.a.c...@googlemail.com>> a écrit :

Hello Mohamed,

Right now this is not possible, and I can't think of any way to
restrict access to system level BLAST databases listed in
the blast*.loc files by user. However, since other Galaxy
tools use *.loc files, someone else may have some ideas.

You might be able to try using a BLAST database in a
shared data library (Galaxy has a role based permissions
system you could use), but the user would first have to
import the database into their current history.

I hope that helps,

Peter

On Thu, Jan 19, 2017 at 1:45 PM, Mohamed Kassam 
<k.mam...@gmail.com<mailto:k.mam...@gmail.com>> wrote:

Dear all,

I would like to know if it is possible to put permission on the macro.xml
for ncbi-blast + database.
For example if I want to show the db to one user and not to all.

Best reagards,

Mohamed

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Re: [galaxy-dev] Blast db permission

2017-01-20 Thread Mohamed Kassam 
Hello Gildas,

Thank you very much for your code.
I will have a look, and come back to you if I have any question.

Best regards,

Mohamed

2017-01-20 10:21 GMT+01:00 Gildas Le Corguillé :

> Hello Mohamed,
>
> Two years ago, we had exactly the same needs (actually, we still have) and
> took an internship to investigate and develop a solution to privatize blast
> databank through Galaxy.
> As many projects, we didn’t find enough time to finalize that.
>
> I have just push the different scripts we have if you want to test or just
> have a look: https://github.com/abims-sbr/galaxy-blastprivate
>
> Cheers
>
> Gildas
>
> -
> Gildas Le Corguillé - Bioinformatician/Bioanalyste
>
> Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
> http://abims.sb-roscoff.fr
>
> Member of the Workflow4Metabolomics project
> http://workflow4metabolomics.org
>
> Station Biologique de Roscoff - UPMC/CNRS - FR2424
> Place Georges Teissier 29680 Roscoff FRANCE
> tel: +33 2 98 29 23 81 <02%2098%2029%2023%2081>
> --
>
>
>
> Le 19 janv. 2017 à 14:53, Peter Cock  a écrit :
>
> Hello Mohamed,
>
> Right now this is not possible, and I can't think of any way to
> restrict access to system level BLAST databases listed in
> the blast*.loc files by user. However, since other Galaxy
> tools use *.loc files, someone else may have some ideas.
>
> You might be able to try using a BLAST database in a
> shared data library (Galaxy has a role based permissions
> system you could use), but the user would first have to
> import the database into their current history.
>
> I hope that helps,
>
> Peter
>
> On Thu, Jan 19, 2017 at 1:45 PM, Mohamed Kassam 
> wrote:
>
> Dear all,
>
> I would like to know if it is possible to put permission on the macro.xml
> for ncbi-blast + database.
> For example if I want to show the db to one user and not to all.
>
> Best reagards,
>
> Mohamed
>
> ___
> 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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Re: [galaxy-dev] Blast db permission

2017-01-20 Thread Gildas Le Corguillé 
Hello Mohamed,

Two years ago, we had exactly the same needs (actually, we still have) and took 
an internship to investigate and develop a solution to privatize blast databank 
through Galaxy.
As many projects, we didn’t find enough time to finalize that.

I have just push the different scripts we have if you want to test or just have 
a look: https://github.com/abims-sbr/galaxy-blastprivate 


Cheers

Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr 

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org 

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
--



> Le 19 janv. 2017 à 14:53, Peter Cock  a écrit :
> 
> Hello Mohamed,
> 
> Right now this is not possible, and I can't think of any way to
> restrict access to system level BLAST databases listed in
> the blast*.loc files by user. However, since other Galaxy
> tools use *.loc files, someone else may have some ideas.
> 
> You might be able to try using a BLAST database in a
> shared data library (Galaxy has a role based permissions
> system you could use), but the user would first have to
> import the database into their current history.
> 
> I hope that helps,
> 
> Peter
> 
> On Thu, Jan 19, 2017 at 1:45 PM, Mohamed Kassam  wrote:
>> Dear all,
>> 
>> I would like to know if it is possible to put permission on the macro.xml
>> for ncbi-blast + database.
>> For example if I want to show the db to one user and not to all.
>> 
>> Best reagards,
>> 
>> Mohamed
>> 
>> ___
>> 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/

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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Re: [galaxy-dev] Blast db permission

2017-01-19 Thread Peter Cock 
Hello Mohamed,

Right now this is not possible, and I can't think of any way to
restrict access to system level BLAST databases listed in
the blast*.loc files by user. However, since other Galaxy
tools use *.loc files, someone else may have some ideas.

You might be able to try using a BLAST database in a
shared data library (Galaxy has a role based permissions
system you could use), but the user would first have to
import the database into their current history.

I hope that helps,

Peter

On Thu, Jan 19, 2017 at 1:45 PM, Mohamed Kassam  wrote:
> Dear all,
>
> I would like to know if it is possible to put permission on the macro.xml
> for ncbi-blast + database.
> For example if I want to show the db to one user and not to all.
>
> Best reagards,
>
> Mohamed
>
> ___
> 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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  https://lists.galaxyproject.org/

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[galaxy-dev] Blast db permission

2017-01-19 Thread Mohamed Kassam 
Dear all,

I would like to know if it is possible to put permission on the macro.xml
for ncbi-blast + database.
For example if I want to show the db to one user and not to all.

Best reagards,

Mohamed
___
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/