Problem referencing EMBOSS tools in universe_wsgi.ini
We have set up our local Galaxy installation to submit jobs by default through HTCondor, using the drmaa tool runner. We override this on a tool-by-tool basis in universe_wsgi.ini, to specify certain tools we always want to run locally. The problem is that EMBOSS tools have a tool id like 'emboss: infoseq46', and it's not possible to reference a tool with an id containing a colon in the universe_wsgi.ini file (because colon is the character which separates a configuration item name from its value). It seems to me there are two possible solutions: 1. Implement some form of escape character processing in the config file parser (on top of Python's ConfigParser) so we can write tool ids in that file like 'emboss%3a infoseq46' 2. Change all the EMBOSS tools to have ids like 'emboss-infoseq46' rather than using a colon and space. For now, we are modifying our XML files locally (with a script) to do 2. Are there any comments from Galaxy developers on which of these solutions they prefer, or any reason why (2) shouldn't be incorporated in the Galaxy mainline? cheers, Simon ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================
On Jan 29, 2013, at 3:59 PM, Guest, Simon wrote:
We have set up our local Galaxy installation to submit jobs by default through HTCondor, using the drmaa tool runner. We override this on a tool-by-tool basis in universe_wsgi.ini, to specify certain tools we always want to run locally.
The problem is that EMBOSS tools have a tool id like ‘emboss: infoseq46’, and it’s not possible to reference a tool with an id containing a colon in the universe_wsgi.ini file (because colon is the character which separates a configuration item name from its value).
It seems to me there are two possible solutions: 1. Implement some form of escape character processing in the config file parser (on top of Python’s ConfigParser) so we can write tool ids in that file like ‘emboss%3a infoseq46’ 2. Change all the EMBOSS tools to have ids like ‘emboss-infoseq46’ rather than using a colon and space.
For now, we are modifying our XML files locally (with a script) to do 2.
Are there any comments from Galaxy developers on which of these solutions they prefer, or any reason why (2) shouldn’t be incorporated in the Galaxy mainline?
Hi Simon, Significant changes to the way that job run parameters are defined will be included in a future release. In specific, there'll be no more job runner URLs, and parameters will be specified with a more robust XML language. These changes aren't stable enough to go out in the next release (scheduled for the end of this week), but they should be in the one after that. --nate
cheers, Simon
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Hi Simon,
Significant changes to the way that job run parameters are defined will be included in a future release. In specific, there'll be no more job runner URLs, and parameters will be specified with a more robust XML language. These changes aren't stable enough to go out in the next release (scheduled for the end of this week), but they should be in the one after that.
--nate
Hi Nate, Thanks for that. We look forward to that release! cheers, Simon -- ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================
participants (2)
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Guest, Simon -
Nate Coraor