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@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. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:[email protected]
