[Bio-linux-list] Updating Bio-Linux

[Tony Travis]

On 01/04/18 11:41, Abdulrahman MI wrote:
> Dear tony
> 
> Thanks for bio-linux 
> I have questions 
> How to update the tools like SPAdes, etc to most recent release.

Hi, Abdulrahman.

You have two options: Compile version 3.11.1 from source:

> http://cab.spbu.ru/software/spades/
Or, use the Debian-Med PPA to install version 3.8.1:

> https://launchpad.net/~debian-med/+archive/ubuntu/ppa

This is what I have installed:

> ajt at beluga:~$ apt-cache policy spades
> spades:
>   Installed: (none)
>   Candidate: 3.8.1+dfsg-1~ubuntu14.04~ppa1
>   Version table:
>      3.8.1+dfsg-1~ubuntu14.04~ppa1 0
>         500 http://ppa.launchpad.net/debian-med/ppa/ubuntu/ trusty/main amd64 Packages

It's very easy to add the Debian-Med PPA to Bio-Linux:

> sudo add-apt-repository ppa:debian-med/ppa
> sudo apt-get update
Please post a message here and on the Debian-Med list if you have any
problems installing or running Spades under Bio-Linux 8 / Ubuntu 14.04.

> and any plan to update the base Ubuntu from 14 to 16?

No, because Ubuntu 18.04 is about to be released, and we will base the
next version of Bio-Linux on Ubuntu-MATE 18.04 LTS. This version will
make use of the Debian-Med team's hard work packaging bioinformatics
software, but will also come with "Bioconda" pre-installed.

Thanks for your interest in Bio-Linux and please help to spread the word
about our Bio-Linux 8.0.8 point release available from:

> http://www.bioinformatics.org/project/?group_id=341

You do not need to re-install Bio-Linux 8.0.7 if you already have it on
your PC hard disk: Just make sure you have updated your installation:

  sudo -i
  apt update
  apt full-upgrade

However, the new Bio-Linux 8.0.8 .iso file has an updated kernel that
better supports modern WiFi chipsets in particular, and all the packages
are updated. The Bio-Linux 8.0.8 .iso also has "mdadm" pre-installed,
which makes installing Bio-Linux to Linux 'md' software RAID easier.

Bye,

  Tony.

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