Question: Installing and running Velvet assembler
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gravatar for annadv77
3.1 years ago by
annadv7720
Canada
annadv7720 wrote:

Dear All,

We were trying to install and run the Velvet tool on our local Galaxy instance. However, we are unable to run the velveth tool: every time we try to do so, we receive the following message:

"an error occurred with this dataset:
Unable to run velveth: No such file or directory"

To install Velvet we were following the steps mentioned in the wiki:

https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial

We were installing the Velvet from the Assembly - VelvetToolSuite, and there were no options mentioning dependencies during the installation to Galaxy. The tools appear to be installed on Galaxy, but when we try to run them (we tried to run only velveth, since the second tool depends on the output of velveth), but every time we are getting the same error, I mentioned earlier in this message.

As we understand, the velveth wrapper calls a utility command "velveth". We are unable to find out how to install that utility command.

 

We would greatly appreciate any advices and help on this subject.

 

Alternatively, is there any other assembler for short DNA sequences we could install on Galaxy?

Thank you very much!

 

Regards,

Anna

assembly velvet • 1.8k views
ADD COMMENTlink written 3.1 years ago by annadv7720
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