Automated reinstall of software from package list

Sun, 20 Nov 2016 00:00:00 +0000

If I need to reinstall a Ubuntu/Debian-based Linux OS (or mirror a software selection to another machine), this is how it can be done. On the source machine:sudpkg --get-selections > ~/Package.listcp -R /etc/apt/sources.list* ~/apt-key exportall > ~/repository.keysThen just copy the files to the target machine:suapt-key add ~/repository.keyscp -R ~/sources.list* /etc/apt/apt-get updateapt-get install dselectdselect updatedpkg --set-selections < ~/Package.listapt-get dselect-upgrade -yIf some packages are not available, this will fail. This concerns in my case manually installed packages like teamviewer or snapgene / snapgene_viewer . I usually remove those packages manually from the list (there are luckily not many of them).However, the upgrade is not fully automatic, since you need to e.g. agree to various licenses (e.g. for Microsoft’s True Type fonts) and acknowledge manually other stuff (e.g. libdvd-pkg legal issues), which kind of defeats the purpose of making this automatic and painless…

The Staden package on Ubuntu for bioinformatics dinosaurs

Wed, 27 Jul 2016 00:00:00 +0000

Mostly we use the SnapGene software when we check the sequences of our DNA constructs. However, sometimes SnapGene’s alignment view is not flexible enough and then I fall back to using the ancient Staden Package . I just had upgraded from Ubuntu 14.04 to 16.04 and hence did not have Staden installed. I was pleasantly surprised when the installation of Staden took only about 15 seconds because finally - thanks to the Debian Med team - Staden is available from the universe repository (actually already since October 2014).sudo apt install stadenStaden is clearly not as intuitive as it could be, but it is very powerful and lends itself to automated processing of data. If you have the opportunity to learn it, I would encourage you to do so. The Finnish CSC recorded the Staden course from 2004, in which I participated and you can get the recordings from Funet TV . I just had briefly considered switching from Ubuntu to SuSE because of the ongoing wireless connection debacle that Canonical can’t seem to fix, but considering how non-trivial a manual install of Staden is, this is a big plus for Ubuntu. There are obviously dedicated Linux distributions for bioinformatics purposes, but they all tend to lag behind the latest and greatest developments of the major distros.

Package on Michael’s Domain

Automated reinstall of software from package list

The Staden package on Ubuntu for bioinformatics dinosaurs