[Bio-linux-dev] Bio-Linux 6 release - thanks to testers

[Tim Booth]

Dear All,

As you would have seen in the announcement yesterday
(http://nebclists.nerc.ac.uk/pipermail/bio-linux-announce/2010-June/000007.html), Bio-Linux 6.0 was released on schedule.  Many thanks to all the people on this list who helped test beta versions of the system and provided feedback.

Please continue to send any questions or suggestions to the helpdesk
address - in many cases we will be able to fix issues with package
updates even if there is a problem with the actual image.

For those running B1 or B2, you do not need to re-install but be aware
of the following issues that will not be fixed by simply upgrading
packages:

     1. Many R libraries are missing off the system.  If you wish to use
        these, they need to be installed manually - full instructions
        are here:
        http://nebc.nerc.ac.uk/tools/bioinformatics-docs/other-bioinf/r-and-bioconductor/?searchterm=cran
     2. You may want to remove firestarter and install gufw as this is
        now the default firewall configurator.
     3. If you use the default automated nightly backups, you should
        update the package and run bio-linux-backup-info to check that
        the settings are correct (see /etc/default/backup).
     4. You can install the bio-linux-tutorials, bio-linux-arb and
        bio-linux-genquery packages which are not on earlier images
     5. You can install maq, velvet and ssake packages which are not on
        the earlier images
     6. You can add the EB-Eye search to Firefox by going to:
        http://www.ebi.ac.uk/inc/help/search_help.html#addebeye
     7. You should setup logcheck as detailed in the user guide, or else
        turn it off to stop daily logcheck mails accumulating
        in /var/mail/spool.
     8. The branding has changed slightly in the final release - startup
        and shutdown logos, login manager and default wallpaper are new.
        This is just cosmetic.
     9. FreeNX server may not work on all beta versions - this can
        normally be fixed by doing 'sudo dpkg-reconfigure -pcritical
        freenx-server'.
    10. Beta 1 did not have the automatic upgrades or update
        notification set up as described in the user guide.  You will
        need to periodically run the update manager to get new
        bioinformatics packages (you would need to do this anyway to get
        Ubuntu updates).
    11. There was an issue with 'umask' setting on B1 - on an installed
        system if you type 'sudo -i' (give password if asked) then
        'umask' you should get 0022.  If you see 0077 then you need to
        run 'sudo visudo' and add the following line at the end of the
        file:

Defaults    umask_override


I hope you enjoy using Bio-Linux 6.

Cheers,

TIM
-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 
at CEH Wallingford
+44 1491 69 2705


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