Re: Bio-Linux 9

[Andreas Tille <andreas@an3as.eu>]

Hi Tony,

On Mon, Oct 15, 2018 at 01:18:15AM +0100, Tony Travis wrote:
> I'm now back from Milan and working part-time at the University of
> Aberdeen again. We are upgrading all our Bio-Linux 8 (Ubuntu 14.04 LTS)
> machines to Ubuntu-MATE 18.04 LTS + med-bio + med-bio-dev as prototypes
> to use during the development of Bio-Linux 9.

This reminds me that I promised to rename the repository.  I renamed it
from biolinux to bio-linux now[1] (to reflect the Vcs fields of your
last commit).
 
> So far the only problem I've encountered is a bug in the "metaphlan2"
> package that I reported here and Andreas acted on. However, the updated
> package is not yet in the Debian Sid repository that Ubuntu is based on.

I admit I have no idea what we can do about this.

> Installing "med-bio" under Ubuntu-MATE 18.04 currently fails installing
> "metaphlan2", but that problem can be resolved by manually installing an
> updated version of the package from a .deb locally.
> 
> I really appreciate the work that the Debian-Med team have been doing to
> incorporate many of the 'missing' packages from Bio-Linux 8 because it
> makes development of Bio-Linux 9 based on Ubuntu-MATE 18.04 LTS and the
> packages from "med-bio" a practical proposition.

You are welcome.  In general we like to support user needs (I admit it
remains a riddle to me why we get so few user requests - it should not
be that hard to write an e-mail and ask for packaging of software xy) and
Bio-Linux is at least a visible user of our work.

I'd recommend to try hard to get the bio-linux package sensible now
pretty soon.  William said he had local changes - please push these way
more frequently.  We should get out bio-linux metapackages **uploaded**
soon to get them really used and tested before the next stable release
will be frozen (if I remember it is only 6 months away and we have left
the package from my initial commit alone since two months).

I'd also love to see the list of missing packages in Debian checked and
enhanced (may be with priorities?) to get even more of the stuff you
need finished.

Kind regards and nice to see you back at your desk ;-)

     Andreas.


[1] https://salsa.debian.org/blends-team/bio-linux
[2] https://salsa.debian.org/med-team/community/bio-linux/blob/master/debian-med_missings.txt

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