What is the correct place under Galaxy for a database that's created by a tool?
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
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 <cline@soe.ucsc.edu> 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/
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/
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 <bjoern.gruening@gmail.com> 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/
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 <bjoern.gruening@gmail.com> 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/
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 <bjoern.gruening@gmail.com> 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 < bjoern.gruening@gmail.com> 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/
participants (3)
-
Björn Grüning -
Melissa Cline -
Peter Cock