configuring job runner for toolshed tools
Is there a way to configure a tool downloaded from the toolshed depot to use a job runner other than the local runner? The tool_id for the toolshed tool isn't honored in universe_wsgi.ini the way the default tools are. Specifically, has anyone configured a toolshed tool to use drmaa instead of localhost? David Hoover Helix Systems Staff
Hi David, I'm not familiar enough with the job runners to know what the problem may be, However, for tools installed from the tool shed, the tool id is the tool-shed generated "guid" instead of the "id" attribute value of the tool config's <tool> tag. So, for example, if you install the freebayes tool shed repository from the main Galaxy tool shed, your tool panel will display the single freebayes tool, which is the only tool contained in the freebayes repository. When this installed tool is loaded into Galaxy, the tools "id" attribute value is: toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.0.2 and the tool's "old_id" attribute value is the value os the "id" attribute in it's tool config <tool> tag: freebayes Have your tried configuring the installed tool using the new id (guid) rather than the old id? I'm not sure if this works, but just wanted to make sure you were using the correct id value. If it still doesn't work, let us know and we'll get a fix asap. Thanks! Greg Von Kuster On Jul 20, 2012, at 5:16 PM, David Hoover wrote:
Is there a way to configure a tool downloaded from the toolshed depot to use a job runner other than the local runner? The tool_id for the toolshed tool isn't honored in universe_wsgi.ini the way the default tools are. Specifically, has anyone configured a toolshed tool to use drmaa instead of localhost?
David Hoover Helix Systems Staff ___________________________________________________________ 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:
I found the guid for the tool and tried the usual method of configuring galaxy to use it via drmaa. With your example, it would be toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.0.2 = drmaa://-l nodes=1/ But this didn't have any effect. It still ran on the localhost. I guess no one has tried this. I haven't tried using the old_id. Would that work? I'd rather not run everything via drmaa, but if the toolshed tools can't be configured, I might have to. David
Hi David,
I'm not familiar enough with the job runners to know what the problem may be, However, for tools installed from the tool shed, the tool id is the tool-shed generated "guid" instead of the "id" attribute value of the tool config's <tool> tag. So, for example, if you install the freebayes tool shed repository from the main Galaxy tool shed, your tool panel will display the single freebayes tool, which is the only tool contained in the freebayes repository.
When this installed tool is loaded into Galaxy, the tools "id" attribute value is:
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.0.2
and the tool's "old_id" attribute value is the value os the "id" attribute in it's tool config <tool> tag:
freebayes
Have your tried configuring the installed tool using the new id (guid) rather than the old id? I'm not sure if this works, but just wanted to make sure you were using the correct id value. If it still doesn't work, let us know and we'll get a fix asap.
Thanks!
Greg Von Kuster
On Jul 20, 2012, at 5:16 PM, David Hoover wrote:
Is there a way to configure a tool downloaded from the toolshed depot to use a job runner other than the local runner? The tool_id for the toolshed tool isn't honored in universe_wsgi.ini the way the default tools are. Specifically, has anyone configured a toolshed tool to use drmaa instead of localhost?
David Hoover Helix Systems Staff ___________________________________________________________ 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:
Hi David, If using the actual tool id (guid) does not work, then it's likely that the job runner code needs to be fixed to correctly handle tools installed from a tool shed. I've created a ticket to get this resolved which you can follow so that you'll receive status changes on the issue. https://bitbucket.org/galaxy/galaxy-central/issue/779/fix-job-runner-to-hand... Thanks for reporting this, and sorry for the inconvenience. Greg Von Kuster On Jul 21, 2012, at 8:29 AM, <hooverdm@helix.nih.gov> wrote:
I found the guid for the tool and tried the usual method of configuring galaxy to use it via drmaa. With your example, it would be
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.0.2 = drmaa://-l nodes=1/
But this didn't have any effect. It still ran on the localhost. I guess no one has tried this.
I haven't tried using the old_id. Would that work?
I'd rather not run everything via drmaa, but if the toolshed tools can't be configured, I might have to.
David
Hi David,
I'm not familiar enough with the job runners to know what the problem may be, However, for tools installed from the tool shed, the tool id is the tool-shed generated "guid" instead of the "id" attribute value of the tool config's <tool> tag. So, for example, if you install the freebayes tool shed repository from the main Galaxy tool shed, your tool panel will display the single freebayes tool, which is the only tool contained in the freebayes repository.
When this installed tool is loaded into Galaxy, the tools "id" attribute value is:
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.0.2
and the tool's "old_id" attribute value is the value os the "id" attribute in it's tool config <tool> tag:
freebayes
Have your tried configuring the installed tool using the new id (guid) rather than the old id? I'm not sure if this works, but just wanted to make sure you were using the correct id value. If it still doesn't work, let us know and we'll get a fix asap.
Thanks!
Greg Von Kuster
On Jul 20, 2012, at 5:16 PM, David Hoover wrote:
Is there a way to configure a tool downloaded from the toolshed depot to use a job runner other than the local runner? The tool_id for the toolshed tool isn't honored in universe_wsgi.ini the way the default tools are. Specifically, has anyone configured a toolshed tool to use drmaa instead of localhost?
David Hoover Helix Systems Staff ___________________________________________________________ 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:
OK, forget what I said earlier. I was watching for a different toolshed tool than what I reconfigured. Never mind, using the guid (the long tool_id shown as an example below) worked correctly. The job was pushed out to the cluster and finished normally. Sorry about the fuss. David On Jul 21, 2012, at 8:40 AM, Greg Von Kuster wrote:
Hi David,
If using the actual tool id (guid) does not work, then it's likely that the job runner code needs to be fixed to correctly handle tools installed from a tool shed. I've created a ticket to get this resolved which you can follow so that you'll receive status changes on the issue.
https://bitbucket.org/galaxy/galaxy-central/issue/779/fix-job-runner-to-hand...
Thanks for reporting this, and sorry for the inconvenience.
Greg Von Kuster
On Jul 21, 2012, at 8:29 AM, <hooverdm@helix.nih.gov> wrote:
I found the guid for the tool and tried the usual method of configuring galaxy to use it via drmaa. With your example, it would be
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.0.2 = drmaa://-l nodes=1/
But this didn't have any effect. It still ran on the localhost. I guess no one has tried this.
I haven't tried using the old_id. Would that work?
I'd rather not run everything via drmaa, but if the toolshed tools can't be configured, I might have to.
David
Hi David,
I'm not familiar enough with the job runners to know what the problem may be, However, for tools installed from the tool shed, the tool id is the tool-shed generated "guid" instead of the "id" attribute value of the tool config's <tool> tag. So, for example, if you install the freebayes tool shed repository from the main Galaxy tool shed, your tool panel will display the single freebayes tool, which is the only tool contained in the freebayes repository.
When this installed tool is loaded into Galaxy, the tools "id" attribute value is:
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.0.2
and the tool's "old_id" attribute value is the value os the "id" attribute in it's tool config <tool> tag:
freebayes
Have your tried configuring the installed tool using the new id (guid) rather than the old id? I'm not sure if this works, but just wanted to make sure you were using the correct id value. If it still doesn't work, let us know and we'll get a fix asap.
Thanks!
Greg Von Kuster
On Jul 20, 2012, at 5:16 PM, David Hoover wrote:
Is there a way to configure a tool downloaded from the toolshed depot to use a job runner other than the local runner? The tool_id for the toolshed tool isn't honored in universe_wsgi.ini the way the default tools are. Specifically, has anyone configured a toolshed tool to use drmaa instead of localhost?
David Hoover Helix Systems Staff ___________________________________________________________ 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:
Back on the topic again, I found another real issue with toolshed tools. I can configure the toolshed tool to be used by drmaa in universe_wsgi.ini, then restart Galaxy and everything's good. However, if I modify the tool .xml file and reload it using the Admin link, it goes back to the default job runner. Can this be changed so that the configured job runner remains the same after reloading the toolshed tool? On Jul 23, 2012, at 5:02 PM, David Hoover wrote:
OK, forget what I said earlier. I was watching for a different toolshed tool than what I reconfigured. Never mind, using the guid (the long tool_id shown as an example below) worked correctly. The job was pushed out to the cluster and finished normally.
Sorry about the fuss.
David
On Jul 21, 2012, at 8:40 AM, Greg Von Kuster wrote:
Hi David,
If using the actual tool id (guid) does not work, then it's likely that the job runner code needs to be fixed to correctly handle tools installed from a tool shed. I've created a ticket to get this resolved which you can follow so that you'll receive status changes on the issue.
https://bitbucket.org/galaxy/galaxy-central/issue/779/fix-job-runner-to-hand...
Thanks for reporting this, and sorry for the inconvenience.
Greg Von Kuster
On Jul 21, 2012, at 8:29 AM, <hooverdm@helix.nih.gov> wrote:
I found the guid for the tool and tried the usual method of configuring galaxy to use it via drmaa. With your example, it would be
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.0.2 = drmaa://-l nodes=1/
But this didn't have any effect. It still ran on the localhost. I guess no one has tried this.
I haven't tried using the old_id. Would that work?
I'd rather not run everything via drmaa, but if the toolshed tools can't be configured, I might have to.
David
Hi David,
I'm not familiar enough with the job runners to know what the problem may be, However, for tools installed from the tool shed, the tool id is the tool-shed generated "guid" instead of the "id" attribute value of the tool config's <tool> tag. So, for example, if you install the freebayes tool shed repository from the main Galaxy tool shed, your tool panel will display the single freebayes tool, which is the only tool contained in the freebayes repository.
When this installed tool is loaded into Galaxy, the tools "id" attribute value is:
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.0.2
and the tool's "old_id" attribute value is the value os the "id" attribute in it's tool config <tool> tag:
freebayes
Have your tried configuring the installed tool using the new id (guid) rather than the old id? I'm not sure if this works, but just wanted to make sure you were using the correct id value. If it still doesn't work, let us know and we'll get a fix asap.
Thanks!
Greg Von Kuster
On Jul 20, 2012, at 5:16 PM, David Hoover wrote:
Is there a way to configure a tool downloaded from the toolshed depot to use a job runner other than the local runner? The tool_id for the toolshed tool isn't honored in universe_wsgi.ini the way the default tools are. Specifically, has anyone configured a toolshed tool to use drmaa instead of localhost?
David Hoover Helix Systems Staff ___________________________________________________________ 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:
___________________________________________________________ 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:
participants (3)
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David Hoover -
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hooverdm＠helix.nih.gov