Re: "med.bio" under Ubuntu-MATE 18.04 LTS

[Andreas Tille <tille@debian.org>]

[Please quote me in public on the list!]

Hi Tony,

On Sat, Jan 05, 2019 at 12:53:15PM +0000, Tony Travis wrote:
> 
> I ran a QIIME2 workshop in Vienna using an alpha version of Bio-Linux 9
> based on Ubuntu-MATE 18.04 LTS + med-bio, med-bio-dev and Bioconda plus
> a few other packages including x2goserver. Everything worked well,

Good to hear!  BTW, I started to work on a QIIME2 package but run into
some trouble and picked up other tasks.  I'd try to pick this up in the
next weeks - but I'd be happy if someone would beat me.

> but
> your update to "metaphlan2" is not available in the Ubuntu repository:
> 
> > root@beluga:~# lsb_release -d
> > Description:	Ubuntu 18.04.1 LTS
> > root@beluga:~# apt policy metaphlan2
> > metaphlan2:
> >   Installed: 2.7.5-2
> >   Candidate: 2.7.5-2
> >   Version table:
> >  *** 2.7.5-2 100
> >         100 /var/lib/dpkg/status
> >      2.7.5-1 500
> >         500 http://gb.archive.ubuntu.com/ubuntu bionic/universe amd64 Packages
> >         500 http://gb.archive.ubuntu.com/ubuntu bionic/universe i386 Packages
> > root@beluga:~# cat /etc/debian_version
> > buster/sid
> 
> Any idea if/when your "metaphlan2" update will arrive in buster/sid?

It is in buster:

$ apt-cache policy metaphlan2
metaphlan2:
  Installiert:           (keine)
  Installationskandidat: 2.7.8-1
  Versionstabelle:
     2.7.8-1 501
        501 http://httpredir.debian.org/debian testing/main amd64 Packages
        501 http://httpredir.debian.org/debian testing/main i386 Packages
         50 http://httpredir.debian.org/debian unstable/main amd64 Packages
         50 http://httpredir.debian.org/debian unstable/main i386 Packages
         50 http://ftp.debian.org/debian unstable/main amd64 Packages
         50 http://ftp.debian.org/debian unstable/main i386 Packages

> For the moment, I'm installing my patched deb to complete any "med-bio"
> installations I do under Ubuntu 18.04 LTS. I did several installations
> while I was in Vienna. I've done many more in Milan and elsewhere too.

We should try to find a method to generate working med-bio in Ubuntu
(which is probably easy by regenerating the source).
 
> Thanks again for all the effort you and the Debian-Med team have put
> into making the 'missing' Bio-Linux packages available in "med-bio".

You are welcome

       Andreas.


-- 
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