[Bio-Linux] Mail3:What is a backport?

[Sasa Paporovic]

To3: What is a backport?

Your Biolinux7-System gather its software from different servers/sources, called repositories.

Some of them are the original repositories for Ubuntu12.04, from which Biolinux is derived.


BTW:

If you want to have a direct look on which repositories are enabled on your system, you find the configuration file in:

/etc/apt/

it is called 

sources.list

,but beware, do not change it manually, I have seen this in Ubuntu answer section

https://answers.launchpad.net/ubuntu

and Ubuntu bugtracker

https://bugs.launchpad.net/ubuntu

to often failing.

One other repository is direct from the Biolinux team and provide the software that makes Biolinux to Biolinux.

The last is:

http://nebc.nerc.ac.uk/bio-linux/

More comfortable you can get a html view of the available software here:

http://nebc.nerc.ac.uk/tools/bio-linux/package-list

Now let us have a look at the original Ubuntu12.04 repositories.

By default following repositories are enabled for Ubuntu 12.04(it is called “Precise pangolin”; Mark Shuttleworth has the tendence to give animal names..., well, no further comment):

deb http://de.archive.ubuntu.com/ubuntu/ precise

[Do not try this in your webbrowser, that will fail. What you see here is apt format]

followed by a space and(not complete list)

main
universe
multiverse
security
backports

Aha, there we have: backports

Let us have a short look at the others:

main:
provide the core of the Ubuntu12.04/Biolinux, like the kernel(linux3.2.x), the unity desktop, LibreOffice,...,
well all what a standard system needs and the Ubuntu Core developers put their hands on.

Universe:
Yes, this is the stuff for us. The brave, the geeks, the... scientists.
Most of the scientific software we use reside in universe.
The packages from the Debian-Med project(you remember:...Tille), for example.

Unfortunately the Ubuntu Core developers do not put hands on this(in general).
The cause is that there is more software out there than developers, so they focus on the main repository to provide a maintained core system.

A other BTW:

If you decide to work on this packages for the benefit of all of us, you can find a software QA page created by the Debian-Med team, that point also to the bugs in Ubuntu bugtracker:

http://qa.debian.org/developer.php?login=debian-med-packaging@lists.alioth.debian.org&ordering=3

and here is a good developer guide to get started:

https://wiki.ubuntu.com/UbuntuDevelopment

[I know Ubuntu best; this is the cause for links to that project. Debian has also good material to get started: have a google]

, but beware. This is the deep look with the long journey. Nothing for a weekend, nothing for short term enthusiasm. You count here in month.
Multiverse:
Here reside the software, where is doubt if it is really free software.
Sometimes it is clear that the Software is non-free. Sometimes the software only depends on non-free components.

Security:
Also Linux is attacable,like through an old browser version. For this and to bypass the common introducing procedure of fixes, which needs a little bit longer, the security repository was introduced.
A small team of the Ubuntu developers are allowed to work direct on this.
For you it is at most relevant for e.g firefox, thunderbird and so on.
Every new version of this by nature security exposed software comes through the security repository.


Uff, finaly we are there. The backports repository.

Backports:
For short: It brings newest software to you. 
Ubuntu(the mother of Biolinux) is at most strictly oriented forward. So, the big bunch of worktime of the Ubuntu Core developers are going into the actual development branch(just finished Ubuntu13.04 raring).
What you get in the older (final) releases, those which are still supported, is what is falling from the desk.
If a fix in the actual development fits also for a problem in one of the previous final releases the patch will also brought there.
The rest of the system of final releases will be kept untouched. There is no special further development on.
On LTS versions, like Ubuntu 12.04(you know it: It is the basis for Biolinux7)the support period is 5 years, in the style described above.

!No newer software will be get into Biolinux in this style!

For getting arround this the backport repository was introduced.

You know, the development of Ubuntu-Linux is more a evolutionary one. There are mostly no hard breaks. You have the opportunity to upgrade from one Ubuntu release version to another. You see this more directly on the distribution upgrade capability from Biolinux6 to Biolinux 7 (based on the upgrade capabilities between Ubuntu 10.04 LTS and Ubuntu12.04 LTS).

And there fits backporting.

Even when you use(and you really should - more stability, better scientific validity through fixes of not obvious calculation/results errors in scientific software) the distribution upgrade, there is a period of waiting around 2 years until you can do that(until the new LTS is final).

For bridging over this gap, we have the backporting repository.

The process of backporting is driven by the community people like you and me and start with looking what is there at software for the latest development branch of Ubuntu(just finished raring, just started saucy).

It follows manually downloading the Package and setting up some  virtualmachines for testing if the package for Raring is also working on older Releases of Ubuntu.

There is a online dokumentation to the backporting process:

https://wiki.ubuntu.com/UbuntuBackports


Ubuntu13.04(just finished development version Raring) → using ubuntu-dev-tools for build for Quantal(Ubuntu12.10) and Precise(Ubuntu12.04) → manually install the result packages in a virtualMachine of Ubuntu12.10 Quantal → manually install the resulting packages in a VirtualMachine of Ubuntu12.04 Precise → use ubuntu-dev-tools to request a backport → prepare the ticket that targets on this on launchpad → if accepted for Ubuntu12.10 Quantal and Ubuntu12.04 Precise → Hits Bilinux 7 through the backports repository


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