[Bio-Linux] Updated QIIME package 1.8.0

[Tony Travis]

On 11/03/14 11:05, Bramwell, Jason wrote:
> Tim,
> What do I have to do to get these (and other) updates? The documentation
> is saying that updates should occur every night but this does not seem
> to be the case for me (689 packaged required yesterday and 689 packages
> still required today). So far I've been running apt-get update/upgrade
> but is this the correct way or is there a 'bio-linux' way of doing this?

Hi, Jason.

You can do 'unattended' upgrades if you want, using the "upgrade-system"
package. This updates the APT database, then downloads and installs
upgrades. However, you *MUST* edit its configuration file or
"upgrade-system" will remove 'redundant' packages too aggressively.
Change the "deborphan" priority to 6:

  sudo -i
  apt-get install upgrade-system
  vim /etc/upgrade-system.conf
  ...
  ORPHANOPTS="--guess-all --libdevel --priority=6"
  ...

The "upgrade-system" command is run daily from:

  /etc/cron.daily/upgrade-system

This only updates the databases, but you can edit it to run
"upgrade-system" once a day by adding the command at the end of the cron
job:

  vim /etc/cron.daily/upgrade-system
  ...
  upgrade-system
  #EOF
  ...

> So far when I update a fresh install there are 689 update packages which
> I can install but then FastTree, Glimmer, Galaxy, Mira and QIIME are
> held back. Am I doing this correctly or should i be following an
> alternate method?

Before you upgrade anything, I recommend installing "aptitude" and using
it to check the consistency of your APT database:

  apt-get install aptitude
  aptitude update
  aptitude -f install

Ubuntu no longer installs "aptitude" by default, but it is recommended
by Debian for managing packages from the command-line:

  https://www.debian.org/doc/manuals/debian-faq/ch-pkgtools.en.html

> 8.1.3 aptitude
>
> aptitude is a package manager for Debian GNU/Linux systems that provides a frontend to the apt package management infrastructure. aptitude is a text-based interface using the curses library, it can be used to perform management tasks in a fast and easy way.
>
> aptitude provides the functionality of dselect and apt-get, as well as many additional features not found in either program:
>
>     aptitude offers easy access to all versions of a package.
>
>     aptitude makes it easy to keep track of obsolete software by listing it under "Obsolete and Locally Created Packages".
>
>     aptitude includes a fairly powerful system for searching particular packages and limiting the package display. Users familiar with mutt will pick up quickly, as mutt was the inspiration for the expression syntax.
>
>     aptitude can be used to install the predefined tasks available. For more information see tasksel, Section 8.1.5.
>
>     aptitude in full screen mode has su functionality embedded and can be run by a normal user. It will call su (and ask for the root password, if any) when you really need administrative privileges
>
> You can use aptitude through a visual interface (simply run aptitude) or directly from the command line. The command line syntax used is very similar to the one used in apt-get. For example, to install the foo package, you can run aptitude install foo.
>
> Note that aptitude is the preferred program for daily package management from console.

You do NOT have to run "aptitude" from a TUI (Full-Screen Text User
Interface). If you want to you can, but I don't recommend it. The main
reason I prefer aptitude is that it is good at fixing broken packages.

HTH,

  Tony.

--
Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
The University of Aberdeen is a charity registered in Scotland, No SC013683.