Installation of SMRTLINK


#1

Hi,

I wanted to install the SMRT-LINK program on an instance, but to be honest following their instructions I cannot get it to work, I have managed to get the tools only package installed, but I would much rather have the gui/server setup if someone could help?

Also any chance we could get it as an install option on the admin page?

Thanks,

Joe


#4

Hi Joe,

The instructions in this topic may be of help to you - Analysing PacBio sequencing data with SMRT Portal on the GVL.

All the best,
Sion


#5

Hi Sion,

Thank you but that is for only analysing data from the RSII platform (which appears to be being phased out), the sequel platform gives different outputs, I can possible convert back to the old format, but having the newest software would be good.

I got the command line only tools but for the installation of the gui it hangs with error message:

Does not have permissions for this directory: /run/user/119/gvfs

Thanks,

Joe


#6

Hi Joe,

I would recommend that you contact Pacific Biosciences about help with the installation. We don’t currently have any plans to provide an install option for SMRT-link, but I will raise it with the other system admins.

As for the error you have encountered. You have full permission to install software as root, so you might want to check if the directory exists (/run/user/119/gvfs).

All the best,
Sion


#7

Hi,

No problem I have managed to get the motif analysis working with the command line tools and I used canu for the assembly.

But I do not have access to that directory at all, have tried giving myself permissions and making myself a superuser to no avail,

Thanks,

Joe


#8

Hi Joe,

I believe the directory is the mount point for GVFS (GNOME Virtual file system) and you should not be able to access it even with sudo. You should direct this query to Pacific Biosciences. I am sure they have a work around.

All the best,
Sion