On 24/06/18 01:21, Charles Plessy wrote: > [...] >> To digress a bit - to care for single packages is a bit from the past. It >> is a requirement, but nothing that a distribution can sell. > > Very much agreed. I see how bioconda is slowly overtaking us, just by > providing an essential feature: the ability to install software via a > package manager without having to ask a busy sysadmin to run a sudo apt > install command.
Hi, Charles. A very important aspect of "Bioconda" is that it provides a solution to 'dependency hell' in which conflicting versions of supporting software for a given pipeline can't be installed on the same system. The issue of having to ask a system admin to install packages is not the main issue. In the case of Bio-Linux 8, I use "Bioconda" to run QIIME for precisely this reason and I intend to pre-install "Bioconda" in Bio-Linux 9. I am also concerned about conflicts between versions of Python, Perl and R libraries installed by the package manager and those installed directly using PiP, CPAN/CRAN. This is the real situation that many of us face. I don't think "Bioconda" is 'overtaking' Debian-Med in the way you suggest. Rather, I see it as a pragmatic solution to a problem that APT struggles to solve using 'alternatives', only one of which can be active at any time - Using multiple "Bioconda" environments as 'ultra-light' containers solves problems without the overhead of "Docker" or VM's. Other, similar, solutions exist to provide multiple environments e.g: > http://modules.sourceforge.net/ I'm a supporter of well-maintained systems based on APT, in which most dependency problems are resolved automatically, but there are still some problems where a neat solution provided by APT does not exist and that's where "Bioconda" et al. provide a reproducible solution instead of the rat's nest of inconsistencies that result from people inappropriately overwriting their APT-managed files using PiP, or CPAN/CRAN manually. 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]
