On 09/07/18 16:12, Michael Crusoe wrote: > > > 2018-07-06 5:16 GMT+03:00 Charles Plessy <[email protected] > <mailto:[email protected]>>: > [...] > the problem with system-wide installations is important enough to be > mentionned multiple times in the Bioconda paper just published in > Nature Methods: > [...]
Hi, Charles and Michael. Bio-Linux is an APT-managed system, and Bio-Linux 9 will be based on "med-bio" and "med-bio-dev". Although I'm running an APT-managed system, I do sometimes find it difficult to live under the constraints imposed by a single dependency tree with incompatible or out-of-date versions of upstream software that I want to use... I 'overload' APT-managed versions by giving precedence to software installed in /usr/local or /opt to avoid breaking the APT dependency tree by introducing package conflicts that can't be resolved. In my view, Bioconda 'environments' are a generalisation of this approach. The core of the system is still APT-managed, but other environments can be superimposed on top of it without breaking the core APT-managed system. What I think would be *good* is to package "Miniconda" for Debian-Med and make it easier to bootstrap "Bioconda": The commonest problem I come across with Bio-Linux is people using CRAN, CPAN or PIP to install files manually as an admin that conflict with packages in the APT-managed part of the filesystem, instead of putting them in /usr/local, /opt or their own home directories - Bioconda provides a solution to that problem. I would like to see us to get the best out of both APT and Bioconda! 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]
