[Bio-linux-list] Future of Bio-Linux (BL 9 & Ubuntu 16.04) ?

Hi All, Just to re-iterate what Tony said, I have a new job up in Edinburgh with a lot to do and a lot to learn. There is nobody in Wallingford to inherit the Bio-Linux project so there is no secret master plan for going forward. My plan is to concentrate fully on my new job for the next few months, then think about my next steps for Bio-Linux once I've settled in the new job. My senior colleagues here are very supportive when I have discussed this with them. In the meantime, I'll be delighted to see any contributions from the user community or ideas of how people want to take things forward, and will participate as much as I can. After all, I'm still a Bio-Linux user myself! I've tried upgrading a Bio-Linux 7 machine to the latest Ubuntu and most things seem to work. Having said that, most of the important packages are already in Ubuntu anyway via Debian-Med, so you could just install vanilla Ubuntu, enable C2D4U to get the R stuff and apt install whatever bioinformatics packages you need. Of course, you won't get package updates either way so you'll be stuck with the current versions of all the tools. The discussion seems to have turned to development details so I'll continue on bio-linux-devel (http://www.bioinformatics.org/mailman/listinfo/bio-linux-devel). TIM On Wed, Jan 20, 2016, at 10:55 PM, Tony Travis wrote: > On 20/01/16 18:01, Andor J Kiss wrote: > > Hello, > > > > Does anyone know the future plans for Bio-Linux? In terms of Bio-Linux > > 9 & Ubuntu 16.04 LTS? > > Hi, Andor. > > I've already volunteered to help keep the Bio-Linux project rolling, but > it is unclear what, if any, continuation of EOS/NEBC funding there might > be to continue supporting Bio-Linux development. > > I think we should let Tim Booth lead the discussion about Bio-Linux 9 > when he has settled into his new job in Edinburgh. > > Meanwhile, we in the Bio-Linux community can continue to provide help > and support for people who want to use the existing Bio-Linux 8. > > I've had good success using Tim's 'upgrade' script to create physical > and virtual Bio-Linux instances based on 'standard' Ubuntu 14.04 LTS: > > > http://environmentalomics.org/bio-linux-installation/ > > wget -qO- http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh | sudo sh > > There are some minor problems with the script, but one show-stopper is > the way Tim's script checks if you have the 'multiverse' repository > enabled in Ubuntu 14.04 LTS. This is how I did it under OpenStack on > iPlant Atmosphere recently: > > > http://www.iplantcollaborative.org/ci/atmosphere > > > Upgrade Ubuntu 14.04.02 LTS base VM to Bio-Linux 8 > > > > # start Ubuntu 14.04.2 no GUI base VM and login > > ajtravis at vm64-212:~$ > > sudo -i > > root at vm64-212:~# > > > > wget http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh > > chmod +x upgrade8.sh > > > > # capture Bio-Linux 8 upgrade script > > vim upgrade8.sh > > ... > > #cd "`mktemp -d || echo /dev/null`" > > #if [ "$?" != 0 ] ; then > > # echo "Unable to change to temporary directory; cannot continue." > > # exit 2 > > #fi > > ... > > ./upgrade8.sh |& tee upgrade8.log > > > > # fix bug when upgrading 'Vanilla' Ubuntu 14.04 > > vim upgrade_to_8.sh > > ... > > # If this was run on a Vanilla Ubuntu 14.04 box then Universe/Multiverse sources > > # will not be active. Tell the user about it. > > if grep -qw universe /etc/apt/sources.list && \ > > grep -qw multiverse /etc/apt/sources.list ; then > > ... > > > > # remove conflicting packages > > apt remove gnome-bluetooth > > > > # upgrade to Bio-Linux 8 > > ./upgrade_to_8.sh |& tee upgrade_to_8.log > > ... > > Err http://archive.ubuntu.com/ubuntu/ trusty/universe prank amd64 0.0.140110-1 > > Could not resolve 'archive.ubuntu.com' > > E: Failed to fetch http://archive.ubuntu.com/ubuntu/pool/universe/p/prank/prank_0.0.140110-1_amd64.deb Could not resolve 'archive.ubuntu.com' > > ... > > > > # restart upgrade > > ./upgrade_to_8.sh > > > > # ubuntu-desktop installed, but not dependencies > > apt remove ubuntu-desktop > > apt install ubuntu-desktop > > > > # tidy up /root > > root at vm64-212:~# > > logout > > ajtravis at vm64-212:~$ > > sudo rm /root/* > > sudo rm /root/.bash_history > > sudo rm -r /root/.config > > sudo rm /root/.viminfo > > sudo ls -al /root > > total 20 > > drwx------ 3 root root 4096 Nov 25 08:50 . > > drwxr-xr-x 23 root root 4096 Nov 25 07:36 .. > > drwx------ 2 root root 4096 Nov 25 08:26 .aptitude > > -rw-r--r-- 1 root root 3106 Feb 19 2014 .bashrc > > -rw-r--r-- 1 root root 140 Feb 19 2014 .profile > > > One way forward is for us to try modifying Tim's Bio-Linux 'upgrade' > script with a view to creating a Debian Bio-Linux meta-package like the > one for "ubuntu-desktop". This will not, of course, provide a new > Bio-Linux 9 'live' DVD, but it would allow us to identify problems and > make remastering an Ubuntu 16.04 LTS .iso image later on much 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:tony.travis at minke-informatics.co.uk > _______________________________________________ > Bio-Linux-list mailing list > Bio-Linux-list at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bio-linux-list -- Of course I'm a technophobe; I program computers for a living!