What is the correct place under Galaxy for a database that's created by a tool?

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What is the correct place under Galaxy for a database that's created by a tool?

Melissa Cline
Hi folks,

Hopefully this is a quick question.  I'm working on a set of tools that will fire off a VM from within Galaxy and will then communicate with the VM.  The VM will create a local database.  The vision is that this won't be a shared database; in a shared Galaxy instance, each user will have his or her own database.  What is the best place to create this database under the Galaxy file system?

Thanks!

Melissa


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Re: What is the correct place under Galaxy for a database that's created by a tool?

Peter Cock
Hi Melissa,

Galaxy expects history datasets to be read only, so the best
option (in term of this data model) might be a (read only)
SQLite database (since it is just a single file on disk). They
could have multiple such databases in their history or
histories.

If you want the user to have just one database and update
it, then things are rather different... I'll let one of the Galaxy
team comment.

Peter

On Tue, Jun 17, 2014 at 12:07 AM, Melissa Cline <[hidden email]> wrote:

> Hi folks,
>
> Hopefully this is a quick question.  I'm working on a set of tools that will
> fire off a VM from within Galaxy and will then communicate with the VM.  The
> VM will create a local database.  The vision is that this won't be a shared
> database; in a shared Galaxy instance, each user will have his or her own
> database.  What is the best place to create this database under the Galaxy
> file system?
>
> Thanks!
>
> Melissa
>
>
> ___________________________________________________________
> 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:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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Re: What is the correct place under Galaxy for a database that's created by a tool?

Björn Grüning-3
In reply to this post by Melissa Cline
Hi Melissa,

Am 17.06.2014 01:07, schrieb Melissa Cline:
> Hi folks,
>
> Hopefully this is a quick question.  I'm working on a set of tools that
> will fire off a VM from within Galaxy and will then communicate with the
> VM.  The VM will create a local database.

Are we talking here about a local Galaxy database or a tool specific
database?

best,
Bjoern

  The vision is that this won't be

> a shared database; in a shared Galaxy instance, each user will have his or
> her own database.  What is the best place to create this database under the
> Galaxy file system?
>
> Thanks!
>
> Melissa
>
>
>
> ___________________________________________________________
> 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:
>    http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/
>
___________________________________________________________
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Re: What is the correct place under Galaxy for a database that's created by a tool?

Melissa Cline
Good thing to clarify: this is a tool-specific database, created by tools that are running inside Galaxy but that should persist after the individual tools are done with their execution.


On Mon, Jun 16, 2014 at 11:23 PM, Björn Grüning <[hidden email]> wrote:
Hi Melissa,

Am 17.06.2014 01:07, schrieb Melissa Cline:

Hi folks,

Hopefully this is a quick question.  I'm working on a set of tools that
will fire off a VM from within Galaxy and will then communicate with the
VM.  The VM will create a local database.

Are we talking here about a local Galaxy database or a tool specific database?

best,
Bjoern


 The vision is that this won't be
a shared database; in a shared Galaxy instance, each user will have his or
her own database.  What is the best place to create this database under the
Galaxy file system?

Thanks!

Melissa



___________________________________________________________
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:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/



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Re: What is the correct place under Galaxy for a database that's created by a tool?

Björn Grüning-3
Hi,

Am 17.06.2014 21:25, schrieb Melissa Cline:
> Good thing to clarify: this is a tool-specific database, created by tools
> that are running inside Galaxy but that should persist after the individual
> tools are done with their execution.

Should it persist as output data or forever even if I start my workflow
from scratch?

What will happen to the db if I reload a tool and rerun it. Will it
extend the database or will it use a new one from scratch?

You have access to the user name if you are running the tool. With that
you can create a table for every user and store your data user-specific.

Cheers,
Bjoern

>
> On Mon, Jun 16, 2014 at 11:23 PM, Björn Grüning <[hidden email]>
> wrote:
>
>> Hi Melissa,
>>
>> Am 17.06.2014 01:07, schrieb Melissa Cline:
>>
>>   Hi folks,
>>>
>>> Hopefully this is a quick question.  I'm working on a set of tools that
>>> will fire off a VM from within Galaxy and will then communicate with the
>>> VM.  The VM will create a local database.
>>>
>>
>> Are we talking here about a local Galaxy database or a tool specific
>> database?
>>
>> best,
>> Bjoern
>>
>>
>>   The vision is that this won't be
>>
>>> a shared database; in a shared Galaxy instance, each user will have his or
>>> her own database.  What is the best place to create this database under
>>> the
>>> Galaxy file system?
>>>
>>> Thanks!
>>>
>>> Melissa
>>>
>>>
>>>
>>> ___________________________________________________________
>>> 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:
>>>     http://lists.bx.psu.edu/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>     http://galaxyproject.org/search/mailinglists/
>>>
>>>
>
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in your mail client.  To manage your subscriptions to this
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Re: What is the correct place under Galaxy for a database that's created by a tool?

Melissa Cline
Hi Björn,

The database should persist "forever", even if the workflow is restarted.  I'm not sure about the distinction between forever and output data, but the database should remain in place until the user takes specific action to make it go away.

If you reload a tool, it will reload/extend the existing database.

If we have access to the user name, and can create user-specific data within one single database, that should address our needs.

Thanks!

Melissa



On Tue, Jun 17, 2014 at 12:32 PM, Björn Grüning <[hidden email]> wrote:
Hi,

Am 17.06.2014 21:25, schrieb Melissa Cline:

Good thing to clarify: this is a tool-specific database, created by tools
that are running inside Galaxy but that should persist after the individual
tools are done with their execution.

Should it persist as output data or forever even if I start my workflow from scratch?

What will happen to the db if I reload a tool and rerun it. Will it extend the database or will it use a new one from scratch?

You have access to the user name if you are running the tool. With that you can create a table for every user and store your data user-specific.

Cheers,
Bjoern



On Mon, Jun 16, 2014 at 11:23 PM, Björn Grüning <[hidden email]>
wrote:

Hi Melissa,

Am 17.06.2014 01:07, schrieb Melissa Cline:

  Hi folks,

Hopefully this is a quick question.  I'm working on a set of tools that
will fire off a VM from within Galaxy and will then communicate with the
VM.  The VM will create a local database.


Are we talking here about a local Galaxy database or a tool specific
database?

best,
Bjoern


  The vision is that this won't be

a shared database; in a shared Galaxy instance, each user will have his or
her own database.  What is the best place to create this database under
the
Galaxy file system?

Thanks!

Melissa



___________________________________________________________
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:
    http://lists.bx.psu.edu/

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:
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