SMRT Analysis v2.2 launched for PacBio platform

[pacbio]

Upgrade to SMRT Analysis v2.2.0 to take advantage of the following new features and improvements:

• Transcriptome Analysis (Iso-Seq™ application) - implementation of full-length transcript QC, clustering, and mapping to a reference using GMAP.
• Long-Amplicon Analysis (for applications such as HLA analysis) - added support for chimera filtering.
• Minor-Variant Analysis - new implementation using a more sophisticated model for variant calling, with sensitivity down to 0.5% frequency.
• HGAP - 10X speed improvement over v2.1 for microbial assembly.
• SMRT Portal Improvements - protocol selection tool, improved graphs and search interfaces.

Please visit our DevNet site to download this latest release.

[sBeier]

I recently installed the current version of SMRTanalysis and am running into a problem:
In SMRTportal, only the original administrator can see any imported SMRTcells, they are invisible to any other user, even if those are set as administrator or scientist, where they should definitely show up.
The SMRTcells imported by a scientist user are also visible to the administrator, but not to the scientist. I checked the access of the mysql-database and it should be fine (and scientists can obviously write to it, just not retrieve the SMRTcells). I have not found any information about this issue, maybe it is a recently introduced one?

Re-checking the view as the original administrator I found that the "user" column for all imported SMRT-cells is empty. Should the SMRTcell be assigned to the user who imported it?

[GenoMax]

SMRTcells start with no group after import. As the admin user you will need to run a job first (e.g. filter-only) to assign SMRTcells to a group. Then that SMRTcell will be visible to that group.

[sBeier]

But shouldn't any admin user be able to do this, not only the "original admin" but also any users I assign to be administrator? I mean, the user that I assigned the role "administrator" can add new users, change portal settings and everything but cannot assign SMRTcells to a group. I would rather be able to have it the other way round, so I can have a "technical admin" and some "analyst admins".

[GenoMax]

Has the "other" administrator tried to assign a group to the SMRTcell (by starting a job)? That is the only way to assign SMRTcells to a group for now, AFAIK.

[sBeier]

The problem is the "other" administrator cannot see any SMRTcells that have not yet been assigned to a group. I was able to make them visible by logging in with the one user called "administrator", that you get during setting up SMRTportal. Any other user I assign the role administrator gets the "Admin" panel, but still cannot see unassigned SMRTcells to be able to assign them. So, for daily work now every time anyone wants to add a SMRTcell, they can, but then they have to log in as "administrator" and assign it to a job. I would rather be able to hide the Admin panel from some users, though without leaving them unable to import and use their own data. I thought the scientist role was meant for this, but it is not.
From this I figured, being able to import a SMRTcell (administrator and scientist) would also mean that you can see and assign it afterwards, but no user beside the original admin can do this.

http://files.pacb.com/software/smrtanalysis/2.0.0/doc/smrtportal/help/Portal_DEF_User_roles.htm

If this was not clear: the SMRTcells are not visible under "SMRTcells available" when creating a new job for any other user than the one called "administrator", not matter what role they have been assigned, not even for ones with the role "administrator". This seems to be the single functionality not available to all administrative users. And this, in turn, seems wrong to me. I solved it by adding the user to the group "all" but it is not clear from documentation, that a user with administrator role does also have to be in this group to effectively be an administrator.
Thanks a lot for helping, genomax, I would not have gotten behind this, without your hints in the right direction!

[GenoMax]

I feel your pain.

We have been trying for years to get PacBio to move in this direction to a defined security model with "roles". The progress has been slow and this is better than previous options (non-existant). As a core we have never felt comfortable making SMRTportal available for general use for this very issue.