Re: [galaxy-dev] Velvet not working

[Simon Gladman]

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 
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 
>>
>> 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_owner_of_a_repository
>> 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 :
>>
>> [0.00] 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:
>>
>>  http://lists.bx.psu.edu/
>
>
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Re: [galaxy-dev] Velvet not working

[Philipe Moncuquet]

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 

> 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_owner_of_a_repository
>
> 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 :
>
> [0.00] 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:
>
>  http://lists.bx.psu.edu/
>
>
>
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Re: [galaxy-dev] Velvet not working

[Greg Von Kuster]

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_owner_of_a_repository

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 :
> [0.00] 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:
> 
>  http://lists.bx.psu.edu/

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[galaxy-dev] Velvet not working

[Philipe Moncuquet]

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 :

[0.00] 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
___
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/