Galaxy with EMBOSS 5 or EMBOSS 6 ?
Dear Galaxians, I am troubleshooting a problem with running EMBOSS infoseq on our local galaxy installation. We are running EMBOSS 6.5. There is a mismatch between the options Galaxy is passing to infoseq (-version), and what infoseq wants (-seqversion). This breaks the tool. While this would be easy to fix in this instance, I wonder if I should be using EMBOSS 5 (which is *really* old, mind you) instead of EMBOSS 6. I suspect with EMBOSS 6 there may be a whole host of similar changes to be made. Can anyone advise? If it turns out that EMBOSS 5 is actually required, perhaps someone could update the relevant info on the Galaxy dependencies page, or at least point me to the place where it says this. cheers, Simon Simon Guest Senior UNIX Technical Consultant AgResearch ======================================================================= 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. =======================================================================
There is a mismatch between the options Galaxy is passing to infoseq (- version), and what infoseq wants (-seqversion). This breaks the tool.
Clarification: I see the -version/-seqversion change to infoseq was made in EMBOSS 6.2.0. I'm still wondering which version I should be using with Galaxy. Maybe 6.1.0 from Jul 2009 is OK? Or should we just fix Galaxy to use the latest and greatest EMBOSS? cheers, Simon PS: Apologies for the crass disclaimer ======================================================================= 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. =======================================================================
Hey Simon, You're right -- the EMBOSS version supported by the Galaxy wrappers is currently EMBOSS 5. We do have a Tool Dependency page here: http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies, but unfortunately while it lists versions for many tools it doesn't cover them all. I'll update the EMBOSS entry. As far as updating the galaxy EMBOSS wrappers to use a newer version, I'm not aware of any plans to do this currently (though someone could certainly do this if so inclined). -Dannon On Jan 28, 2013, at 3:10 PM, "Guest, Simon" <Simon.Guest@agresearch.co.nz> wrote:
Dear Galaxians,
I am troubleshooting a problem with running EMBOSS infoseq on our local galaxy installation. We are running EMBOSS 6.5.
There is a mismatch between the options Galaxy is passing to infoseq (-version), and what infoseq wants (-seqversion). This breaks the tool.
While this would be easy to fix in this instance, I wonder if I should be using EMBOSS 5 (which is *really* old, mind you) instead of EMBOSS 6. I suspect with EMBOSS 6 there may be a whole host of similar changes to be made.
Can anyone advise?
If it turns out that EMBOSS 5 is actually required, perhaps someone could update the relevant info on the Galaxy dependencies page, or at least point me to the place where it says this.
cheers, Simon
Simon Guest Senior UNIX Technical Consultant AgResearch
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You're right -- the EMBOSS version supported by the Galaxy wrappers is currently EMBOSS 5. We do have a Tool Dependency page here: http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies, but unfortunately while it lists versions for many tools it doesn't cover them all. I'll update the EMBOSS entry.
Hi Dannon, Thanks. After a bit more looking around, I also found the version in the tool_conf.xml file, which confirmed I need to install EMBOSS 5.0.0.
As far as updating the galaxy EMBOSS wrappers to use a newer version, I'm not aware of any plans to do this currently (though someone could certainly do this if so inclined).
We may do this ourselves, and contribute the updates. First we'll get it all rolled out with EMBOSS 5. Later on I may be back in touch about how we can contribute updates into 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. =======================================================================
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Dannon Baker -
Guest, Simon