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

[Tony Travis]

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.

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