Bio-Linux is a specialised Linux disro that provides both standard and cutting edge bioinformatics software tools on a Linux base.
I wrote a post on my old blog a little while back now detailing how to use the packages from Bio-Linux in Ubuntu Linux, but it got missed in the migration (sorry to all those who have been searching for it). Here’s a repost and update for Ubuntu 7.10…
Log into your system and open up a terminal, then follow these steps…
sudo gedit /etc/apt/sources.list
Add the following lines to the end of the file:
# Bio-Linux package repository
deb http://envgen.nox.ac.uk/bio-linux/ unstable bio-linux
Save and close the file, now back at the terminal type the following:1
sudo apt-get update
sudo apt-get install bio-linux-base-directories bio-linux-staden
Next step is to set-up your environment for Bio-Linux…
sudo gedit /etc/bash.bashrc
Add the following lines to the end of the file:
# Set up Bio-Linux Environment
source /usr/local/bioinf/config_files/aliasrc
source /usr/local/bioinf/config_files/bioenvrc
Save and close the file.
That’s it, now all of the packages available through Bio-Linux are now available to you in Ubuntu. One final word of warning… I’ve noticed that a few of the packages are a little out of date, (the Bio-Linux version of Taverna is 1.4, but 1.7 is now available)2 so it might be worth checking the version numbers before installing things.
-
Note that we need to install the
bio-linux-stadenpackage, without this we’d have to do a bit more hacking in config files to stop getting errors whenever we open up a terminal. ↩ -
The other thing to note with the Bio-Linux version of Taverna - it doesn’t start properly without a little bit of hacking…
(If you decided to go with the Bio-Linux version, you can launch it by running the following in the terminal: /usr/local/bioinf/taverna/taverna/runme.sh). ↩
is it same way to install the deb packages in AMD64 bit Ubuntu ? b’coz the deb packages are for i386 ??? will it work ?
Short answer… no idea - never tried to use these packages on 64-bit Ubuntu.
In theory your processor should be able to run the code (as both AMD and Intel 64-bit chips can run 32-bit code), but you will probably not have all of the required (32-bit) supporting libraries for things to work smoothly.
What packages were you after? You might be able to get native 64-bit packages elsewhere.
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I have this error: NO_PUBKEY 3EC653D3EADA2460 How can I import the pubblic key? Thank you in advance Andrea
Hi @andrea, it’s been a while since I used bio-linux (or even Ubuntu on the desktop), but I seem to remember if you follow the instructions here (installing the packages via synaptic) I think synaptic will take care of the keys for you. Hope this helps!
Thank you Daz, unfortunately using synaptic I have the same problem. Adding repositories to source.list it’s not enough, if I don’t import the pubblic key the new repositories are not available.