[Bio-Linux] Bio-Linux 8 small fixes (Tim Booth)

[Tim Booth]

Hi Steve,

I never really thought about this as I always use PostgreSQL wherever I
can.  We used to ship some tools that needed MySQL installed but given
they are pretty much obsolete I might just take MySQL off the image
entirely and people can "apt-get install" what they actually want.

By the way, if anyone else needs to tinker with the script in a similar
way, just set UNPACK_ONLY before you run it - eg.

$ env UNPACK_ONLY=1 runurl http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh

The script will say:
...
Unpack complete in /tmp/tmp.3NynzJEmL8. Exiting.

Then:

$ mv /tmp/tmp.3NynzJEmL8 ./upgrader_unpacked
$ cd ./upgrader_unpacked
$ sudo bash ./upgrade_to_8.sh

Cheers,

TIM

> This probably won't affect most, but I use MariaDB rather than MySQL,
> which caused errors with the update. I needed to extract the files
> from upgrade8.sh using sharutils and edit the
> bl_master_package_list.txt to replace mysql-client etc. with
> mariadb-client etc..
> 
> I'd personally recommend everyone use MariaDB (a fork and drop in
> replacement of MySQL developed by SkySQL), with the plans that the
> evil Oracle no doubt have for MySQL in the long run.
> 
> Cheers,
> 
> Steve
> 
> 
> On 6 August 2014 12:00, <bio-linux-request at nebclists.nerc.ac.uk>
> wrote:
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>            1. Bio-Linux 8 small fixes (Tim Booth)
>         
>         
>         ----------------------------------------------------------------------
>         
>         Message: 1
>         Date: Tue, 5 Aug 2014 19:21:46 +0100
>         From: Tim Booth <tbooth at ceh.ac.uk>
>         To: Bio-Linux mailing list <bio-linux at nebclists.nerc.ac.uk>
>         Subject: [Bio-Linux] Bio-Linux 8 small fixes
>         Message-ID: <1407262906.6360.225.camel at balisaur>
>         Content-Type: text/plain; charset="UTF-8"
>         
>         Dear Bio-Linux users,
>         
>         Since the release of Bio-Linux 8 I've had a few people
>         reporting minor
>         glitches with the system, which I've been working to address,
>         but
>         generally feedback has been good. :-)
>         
>         This is to let you know that I just put up a new ISO (and
>         matching OVA)
>         today that incorporates various small fixes, and most
>         significantly
>         restores the bioinformatics Dash menu so that you can more
>         conveniently
>         access all the tools (or at least the GUI tools) on the
>         system.
>         
>         See this if you're not sure what I mean:
>         http://nebc.nerc.ac.uk/downloads/bl8_only/biomenu.png
>         
>         If you are already running BL8, to be sure you get the fixes
>         you should
>         run the upgrade script again (this also applies if you
>         installed BL8
>         directly) :
>         
>         sudo apt-get install runurl
>         sudo runurl
>         http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh
>         (and reboot)
>         
>         The script is designed to only install stuff it sees is
>         missing, so if
>         the system is already up-to-date it should finish in around a
>         minute and
>         then report "All done - your system is updated to Bio-Linux
>         8".
>         
>         Cheers,
>         
>         TIM
>         
>         --
>         Tim Booth <tbooth at ceh.ac.uk>
>         NERC Environmental Bioinformatics Centre
>         
>         Centre for Ecology and Hydrology
>         Maclean Bldg, Benson Lane
>         Crowmarsh Gifford
>         Wallingford, England
>         OX10 8BB
>         
>         http://nebc.nerc.ac.uk
>         +44 1491 69 2705
>         
>         
>         ------------------------------
>         
>         Subject: Digest Footer
>         
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>         ------------------------------
>         
>         End of Bio-Linux Digest, Vol 71, Issue 9
>         ****************************************
> 
> 
> 
> -- 
>  
> Steve Moss
> about.me/gawbul
> Steve Moss on about.me
>  

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705