[Bio-linux-list] QIIME2 under Bio-Linux 8

[Tony Travis]

On 04/08/17 11:48, Tim Booth wrote:
> [...]
> On Thu, 2017-08-03 at 20:49 +0000, Simon Creer wrote:
>> [...]
>> Before I start trying to reinstall QIIME2 on my existing BioLinux
>> sticks I wanted to touch base with you first, to explore whether or
>> not you thought there were better options available? Either because
>> you are already updating BioLinux with Q2 and could let me have some
>> new sticks, or because you may have a more streamlined solution into
>> getting Q2 onto my existing ones?
>> Hoping that you get this mail and if you could get back to me at your
>> earliest convenience, I would be really grateful, many thanks!

Hi, Simon.

Tim forwarded your email to me and I've CC'ed it to the Bio-Linux list
in case anyone else is struggling with QIIME under Bio-Linux.

I installed QIIME 1.9.1 using "bioconda" under Bio-Linux 8.0.7 a while
ago, when helping a colleague who was having problems with the version
installed by default. This is how to install QIIME using "bioconda":

> # install Miniconda to /usr/local/miniconda2
> wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
> bash Miniconda2-latest-Linux-x86_64.sh
> 
> # configure Miniconda for Python 2.7
> export PATH="/usr/local/miniconda2/bin:$PATH"
> conda config --add channels conda-forge
> conda config --add channels defaults
> conda config --add channels r
> conda config --add channels bioconda
> 
> # install QIIME
> conda install qiime
> print_qiime_config.py -t

I then wrote a "wrapper" to prevent "bioconda" breaking the default
Ubuntu 14.04 Python environmment used by Bio-Linux:

> root at wildcat:~# cat /usr/local/bin/bioconda
> #!/bin/bash
> #@(#)bioconda.sh  2017-08-08  A.J.Travis
> 
> #
> # Wrapper for Bioconda Python environment
> #
> 
> # check if already in Bioconda environment
> export BIOCONDA_HOME=/usr/local/miniconda2
> if [[ "$PATH" != *$BIOCONDA_HOME* ]]; then
> 
> 	# added by Miniconda2 4.3.11 installer
> 	export PATH="$BIOCONDA_HOME/bin:$PATH"
> 	debian_chroot=bioconda exec /bin/bash
> fi

You can then run my "bioconda" wrapper to install and use conda:

> root at wildcat:~# bioconda
> (bioconda)root at wildcat:~# 
> conda list qiime
> # packages in environment at /usr/local/miniconda2:
> #
> qiime                     1.9.1               np112py27_1    bioconda
> qiime-default-reference   0.1.3                    py27_0    bioconda

I've followed the instructions to install QIIME2 in bioconda at:

> https://docs.qiime2.org/2017.7/install/native/

This is how I installed it using my "bioconda" wrapper:

> (bioconda)root at wildcat:~# 
> bioconda
> conda update conda
> conda create -n qiime2-2017.7 --file https://data.qiime2.org/distro/core/qiime2-2017.7-conda-linux-64.txt
> source activate qiime2-2017.7

> (bioconda)root at wildcat:~# source activate qiime2-2017.7
> (qiime2-2017.7) (bioconda)root at wildcat:~# conda list qiime2
> # packages in environment at /usr/local/miniconda2/envs/qiime2-2017.7:
> #
> qiime2                    2017.7.0                 py35_0    qiime2/label/r2017.7

The "qiime command now defaults to QIIME2:

> (qiime2-2017.7) (bioconda)root at wildcat:~# qiime --version
> q2cli version 2017.7.0
> Run `qiime info` for more version details.

We've created a Bio-Linux 8.0.8 point-release and are testing the .iso:
I can supply Bio-Linux 8.0.8 sticks commercially if you are interested?

HTH,

  Tony.

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