Blast db permission

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Blast db permission

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

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Re: Blast db permission

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 <[hidden email]> 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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Re: Blast db permission

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 <[hidden email]> 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 <[hidden email]> 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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Re: Blast db permission

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 <[hidden email]>:
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: <a href="tel:02%2098%2029%2023%2081" value="+33298292381" target="_blank">+33 2 98 29 23 81
------------------------------------------------------------------



Le 19 janv. 2017 à 14:53, Peter Cock <[hidden email]> 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 <[hidden email]> 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/

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 http://galaxyproject.org/search/mailinglists/
___________________________________________________________
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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: Blast db permission

SAPET, Frederic
In reply to this post by Gildas Le Corguillé

Hello,

 

I have also the same needs !

 

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

 

Something like this :

 

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

    <param name="refset" type="select" label="the query sequences blast formated database" help="if your genome of interest is not listed - contact Bioinfo team">

                <options from_data_table="blastdb_private" />

    </param>

#else

    <param name="refsetp" type="select" label="the query sequences blast formated database" help="if your genome of interest is not listed - contact Bioinfo team">

                <options from_data_table="blastdb_public" />

    </param>

#end if

 

 

Fred

 

De : galaxy-dev [mailto:[hidden email]] De la part de Gildas Le Corguillé
Envoyé : vendredi 20 janvier 2017 10:22
À : Peter Cock <[hidden email]>
Cc : Galaxy Dev List <[hidden email]>
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

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 <[hidden email]> 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 <[hidden email]> 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
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
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