[Bio-linux-list] Updated to Ubuntu 16.04 and now I am having problems with qiime

[David Bradshaw]

Dear Tony Travis,

I tried following your script above but it does not seem to recognize that
the biolinux version exists. Please see below. Sorry, I am still a bit new
to the qiime and linux systems. What would be the next step?

microbiology at microbiology-OptiPlex-9020[microbiology] sudo apt-cache policy
python-skbio
python-skbio:
  Installed: 0.4.1-1
  Candidate: 0.4.1-1
  Version table:
 *** 0.4.1-1 500
        500 http://us.archive.ubuntu.com/ubuntu xenial/universe amd64
Packages
        100 /var/lib/dpkg/status
microbiology at microbiology-OptiPlex-9020[microbiology] sudo apt install
python-skbio=0.2.3-0biolinux2
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Version '0.2.3-0biolinux2' for 'python-skbio' was not found
microbiology at microbiology-OptiPlex-9020[microbiology]
[10:12AM]

Thank you for your time and help,

Sincerely,

David Bradshaw

On Sat, Aug 13, 2016 at 12:20 PM, Tony Travis <
tony.travis at minke-informatics.co.uk> wrote:

> On 12/08/16 21:00, David Bradshaw wrote:
> > Dear Whom It May Concern,
> >
> > I may have accidentally sent this email to the wrong place initially, I
> > apologize. I upgraded to Ubuntu 16.04 and now there are items within
> > qiime that are not working. I imagine I may have removed some essential
> > items during the upgrade? What would be the best way to fix this? Below
> > are some of the errors I am encountering with the print_qiime_config_all
> > and join_paired_ends commands.
>
> Hi, David.
>
> I've also upgraded Bio-Linux 8 on my laptop "beluga" to Ubuntu 16.04 LTS
> and there are a few problems: I've confirmed your bug report, which is
> caused by the "xenial" (16.04) version of python-skbio taking
> prece4dence over Tim's Bio-Linux version:
>
> > root at beluga:~# apt-cache policy python-skbio
> > python-skbio-doc:
> >   Installed: (none)
> >   Candidate: 0.4.1-1
> >   Version table:
> >      0.4.1-1 500
> >         500 http://gb.archive.ubuntu.com/ubuntu xenial/universe amd64
> Packages
> >         500 http://gb.archive.ubuntu.com/ubuntu xenial/universe i386
> Packages
> > python-skbio:
> >   Installed: 0.4.1-1
> >   Candidate: 0.4.1-1
> >   Version table:
> >  *** 0.4.1-1 500
> >         500 http://gb.archive.ubuntu.com/ubuntu xenial/universe amd64
> Packages
> >         100 /var/lib/dpkg/status
> >      0.2.3-0biolinux2 500
> >         500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty/main
> amd64 Packages
>
> Force the version to make "apt" downgrade to the Bio-Linux 8 version:
>
> > root at beluga:~# apt install python-skbio=0.2.3-0biolinux2
> > Reading package lists... Done
> > Building dependency tree
> > Reading state information... Done
> > The following packages were automatically installed and are no longer
> required:
> >   python-bz2file python-cachecontrol python-contextlib2 python-requests
> > Use 'sudo apt autoremove' to remove them.
> > The following packages will be DOWNGRADED:
> >   python-skbio
> > 0 to upgrade, 0 to newly install, 1 to downgrade, 0 to remove and 0 not
> to upgrade.
> > Need to get 257 kB of archives.
> > After this operation, 1,953 kB disk space will be freed.
> > Do you want to continue? [Y/n]
> > Get:1 http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty/main amd64
> python-skbio amd64 0.2.3-0biolinux2 [257 kB]
> > Fetched 257 kB in 0s (715 kB/s)
> > dpkg: warning: downgrading python-skbio from 0.4.1-1 to 0.2.3-0biolinux2
> > (Reading database ... 522743 files and directories currently installed.)
> > Preparing to unpack .../python-skbio_0.2.3-0biolinux2_amd64.deb ...
> > Unpacking python-skbio (0.2.3-0biolinux2) over (0.4.1-1) ...
> > Setting up python-skbio (0.2.3-0biolinux2) ...
> > root at beluga:~# apt-cache policy python-skbio
> > python-skbio:
> >   Installed: 0.2.3-0biolinux2
> >   Candidate: 0.4.1-1
> >   Version table:
> >      0.4.1-1 500
> >         500 http://gb.archive.ubuntu.com/ubuntu xenial/universe amd64
> Packages
> >  *** 0.2.3-0biolinux2 500
> >         500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty/main
> amd64 Packages
> >         100 /var/lib/dpkg/status
> >
>
> There are still many problems with the OpenMPI support for QIIME, but at
> least this is a step in the right direction :-)
>
> HTH,
>
>   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:tony.travis at minke-informatics.co.uk
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