Re: Digressions (Re: Bio-Linux 9)
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.
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