Hi developers,
We have our own instance running and under continuoius development. I installed velvetg and velveth from the toolshed (revision 0:4afe13ac23b6http://toolshed.g2.bx.psu.edu/repository/view_changelog?id=9dca5b8f68c509af) and manually installed binaries for velvet_1.2.08. When I try to test it under the galaxy web interface, the job does not failed but all files are empty except the first one that contains the following error message :
[0.000000] Unknown option: -ins_length3
I guess this might come from the version of the binaries and the version the xml wrapper was written for are different. Does anyone knows which binaries version I should use ?
How is it that the job does not appears as failed ? Any help will greatly appreciated.
Regards,
Philippe
Hi Phillippe,
You may have better luck in getting a response to this if you contact the owner of the repository you installed from the tool shed. See this wiki page for details on how to do this.
http://wiki.galaxyproject.org/ToolShedRepositoryFeatures#Contacting_the_owne...
Greg Von Kuster
On Nov 7, 2012, at 6:29 PM, Philipe Moncuquet wrote:
Hi developers,
We have our own instance running and under continuoius development. I installed velvetg and velveth from the toolshed (revision 0:4afe13ac23b6) and manually installed binaries for velvet_1.2.08. When I try to test it under the galaxy web interface, the job does not failed but all files are empty except the first one that contains the following error message : [0.000000] Unknown option: -ins_length3 I guess this might come from the version of the binaries and the version the xml wrapper was written for are different. Does anyone knows which binaries version I should use ? How is it that the job does not appears as failed ? Any help will greatly appreciated. Regards, Philippe ___________________________________________________________ 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:
Thanks for the tip. I have already done this but not via galaxy toolshed (always good to learn new stuff). I didn't get any answers so far, so I hoped to be luckier on the dev list. Thanks again for quick reply.
2012/11/8 Greg Von Kuster greg@bx.psu.edu
Hi Phillippe,
You may have better luck in getting a response to this if you contact the owner of the repository you installed from the tool shed. See this wiki page for details on how to do this.
http://wiki.galaxyproject.org/ToolShedRepositoryFeatures#Contacting_the_owne...
Greg Von Kuster
On Nov 7, 2012, at 6:29 PM, Philipe Moncuquet wrote:
Hi developers,
We have our own instance running and under continuoius development. I installed velvetg and velveth from the toolshed (revision 0:4afe13ac23b6http://toolshed.g2.bx.psu.edu/repository/view_changelog?id=9dca5b8f68c509af) and manually installed binaries for velvet_1.2.08. When I try to test it under the galaxy web interface, the job does not failed but all files are empty except the first one that contains the following error message :
[0.000000] Unknown option: -ins_length3
I guess this might come from the version of the binaries and the version the xml wrapper was written for are different. Does anyone knows which binaries version I should use ?
How is it that the job does not appears as failed ? Any help will greatly appreciated.
Regards,
Philippe
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 Philipe,
Unfortunately, the velvet wrappers in the toolshed seem to be very specific to a certain compilation of velvet. You'll need to recompile Velvet locally with the same settings. I think it needs CATEGORIES=5 in the make command for velvet.
Hope this helps,
Simon Gladman VBC - Monash University & Victorian Life Sciences Computation Initiative
On Thursday, 8 November 2012, Philipe Moncuquet philippe.mcqt@gmail.com wrote:
Thanks for the tip. I have already done this but not via galaxy toolshed
(always good to learn new stuff). I didn't get any answers so far, so I hoped to be luckier on the dev list.
Thanks again for quick reply.
2012/11/8 Greg Von Kuster greg@bx.psu.edu
Hi Phillippe, You may have better luck in getting a response to this if you contact
the owner of the repository you installed from the tool shed. See this wiki page for details on how to do this.
http://wiki.galaxyproject.org/ToolShedRepositoryFeatures#Contacting_the_owne...
Greg Von Kuster
On Nov 7, 2012, at 6:29 PM, Philipe Moncuquet wrote:
Hi developers, We have our own instance running and under continuoius development. I installed velvetg and velveth from the toolshed
(revision 0:4afe13ac23b6) and manually installed binaries for velvet_1.2.08.
When I try to test it under the galaxy web interface, the job does not
failed but all files are empty except the first one that contains the following error message :
[0.000000] Unknown option: -ins_length3
I guess this might come from the version of the binaries and the version
the xml wrapper was written for are different. Does anyone knows which binaries version I should use ?
How is it that the job does not appears as failed ? Any help will
greatly appreciated.
Regards,
Philippe
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:
galaxy-dev@lists.galaxyproject.org
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Greg Von Kuster -
Philipe Moncuquet -
Simon Gladman