Hi,

there is a bug in the install script for Ubuntu 16.04.

Just follow the next lines to install the obitools :

## go to your home dir or wherever you want
cd

## create a virtual env with python 2.7
mkdir OBI
cd OBI
virtualenv-2.7 OBI-env

## get and extract the source
wget 'https://git.metabarcoding.org/obitools/obitools/repository/archive.tar.gz?ref=master'
tar -zxvf "archive.tar.gz?ref=master"

## activate the virtual env
source OBI-env/bin/activate

## last sphinx version has a problem, install one that is OK
pip install sphinx==1.4.8

## enter the source folder
cd obitools-master-*

## build the package
python setup.py build

## install it in the virtual env
python setup.py install

## leave the virtualenv
deactivate

At this point the software should be installed within the OBI directory, just add the bin directory in your PATH

## add this line in your .bashrc
## to enable the OBITools

export PATH=${PATH}:"~/OBI/OBI-env/bin"

regards

Hello I tried all the above suggestion but no luck. But someone helped me and I would like to share how it worked for me.

1) First, you need to install pip, in case you don't have it:

sudo apt-get install python-pip

2) Then install the biopython dependencies:

sudo pip install biopython

3) Then, simply install the OBITools python package. It will automatically install virtualenv, cython and sphinx:

sudo pip install obitools

(Probably, you will get some warnings and "compiling errors". But the OBITools will still work.)

To test if the OBITools have been properly installed, then try to write in the command line, for example:

obicount --help

And if you get the help screen of the command, then everything's working OK.

I hope it will work for you

The answer above also solved my problem once (thanks!), but when I tried to install it on Ubuntu 16 LTS, it didn t work any more. Error:

error in OBITools setup command: 'install_requires' must be a string or list of strings containing valid project/version requirement specifiers; Invalid requirement, parse error at "'and <6'"

In a bioinformatics group I got the message that apparently, there is a bug in the installation script of OBITools when run in Ubuntu 16.

One way was to go back to Ubuntu 14, but that s not a good long term solution.

If you are not averse to running a tool from docker, containerized obitools is now available (I'm the author of the repository): https://hub.docker.com/r/romunov/obitools

You can use Python to send it commands, or just regular docker exec ....