[Bio-linux-list] How to update mothur?

[Tony Travis]

On 31/01/17 09:32, Maxime GOMMEAUX wrote:
> Dear users of Bio-Linux,
> 
> I have been an enthusiastic user of the Bio-Linux distribution for
> ~2years and I appreciate it greatly.

Hi, Maxime.

I'm glad you like Bio-Linux :-)

> I would like, however, to update the mothur package to try their new
> clustering algorithm, included in the brand-new release 1.39.

OK, but this version is NOT yet packaged for Debian/Ubuntu and, as you
probably already know, you have to get it from GitHub:

> https://github.com/mothur/mothur/releases/tag/v1.39.0

[The repository also contains updated binaries of supporting programs]

> If I remember well, originally the version of mothur was 1.34 at the
> time I installed the distro. Some time later it upgraded to 1.36
> "automatically" (with the normal system updates), but it has been stuck
> since then.

You're right that the current version is 1.36:

> root at wildcat:~# apt-cache policy mothur
> mothur:
>   Installed: 1.36.1+dfsg-0biolinux1
>   Candidate: 1.36.1+dfsg-0biolinux1
>   Version table:
>  *** 1.36.1+dfsg-0biolinux1 0
>         500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main amd64 Packages
>         100 /var/lib/dpkg/status
>      1.31.2+dfsg-2build1 0
>         500 http://gb.archive.ubuntu.com/ubuntu/ trusty/universe amd64 Packages
>      1.22.2-2 0
>         500 http://archive.ubuntu.com/ubuntu/ precise/universe amd64 Packages
> root at wildcat:~# 

This is because Tim Booth, the lead developer, has now left the project
and I am seeking funding to continue it. However, I'm just answering any
queries on the Bio-Linux list at present not updating packages.

> Thus, I would like to update mothur "manually", but I don't want to
> wreck my system. Remark: the Ubuntu base is still 14.04 (I have refused
> the 16.04 upgrade to date, but maybe I should do this first???).

I've upgraded several Bio-linux 8 Ubuntu 14.04 LTS instances to 16.04
LTS, but many packages break and I don't recommend doing that unless you
are prepared to enter 'package-dependency-hell' :-(

Even if you did, you would get the same version of "mothur". This is on
my Bio-Linux 8 laptop "beluga", which I've upgraded to Ubuntu 16.04 LTS:

> ajt at beluga:~$ lsb_release -d
> Description:	Ubuntu 16.04.1 LTS
> ajt at beluga:~$ apt-cache policy mothur
> mothur:
>   Installed: (none)
>   Candidate: 1.36.1+dfsg-0biolinux1
>   Version table:
>      1.36.1+dfsg-0biolinux1 500
>         500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu trusty/main amd64 Packages
>      1.36.1-1build1 500
>         500 http://gb.archive.ubuntu.com/ubuntu xenial/universe amd64 Packages

I've not installed "mothur" because of the 'package-dependency-hell'...

If you want to try updating "mothur" manually under Bio-Linux 8 (Ubuntu
14.04), download the binaaries from GitHub:

> wget https://github.com/mothur/mothur/releases/download/v1.39.0/Mothur.linux_64.zip

Then extract it and install just the "mothur" binary:

> unzip Mothur.linux_64.zip
> ls -R mothur
> mothur:
> blast  CatchAllCmdL.exe  LICENSE  mothur  uchime  vsearch
> 
> mothur/blast:
> bin
> 
> mothur/blast/bin:
> bl2seq  blastall  blastclust  blastpgp  copymat  fastacmd  formatdb  formatrpsdb  impala  makemat  megablast  rpsblast  seedtop
> cp -ai mothur/mothur /usr/local/bin/

This will place the updated version of "mothur" ahead of the previously
installed version on your PATH:

> which -a mothur
> /usr/local/bin/mothur
> /usr/bin/mothur

Try running this version, but you may need to copy other supporting
binaries from the .zip file into /usr/local/bin. However, that may well
break other things in Bio-Linux, especially QIIME...

> Thank you for any help!

OK, let me know how you get on?

Thanks,

  Tony.

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