Traitar installation issue

Question

[112498262]

I am trying to install the Traitar (microbial trait analyzer) software on Biolinux8 running on a virtual box. When I install Traitar with pip I get the following error;

ImportError: Tornado requires an up-to-date SSL module. This means Python 2.7.9+ or 3.4+ (although some distributions have backported the necessary changes to older

Has anyone has had this issue and found a solution?

[Joe]

Try:

python -m pip install --upgrade python

You may also need to upgrade pip first:

python -m pip install --upgrade pip

It will usually emit a warning if there's a newer version anyway.

Alternatively, download the latest conda installer, and use conda's python binary from hereon.

https://conda.io/docs/download.html

[GenoMax]

What version of python are you running? What is the output of python -V or python3 -V?

[112498262]

Python version 2.7.6

[GenoMax]

Then upgrade your python to v.2.7.9+ as suggested above.

[112498262]

Thnaks, I have tried that. When I type python3 -V I get Python 3.4.3, so I'm not sure which one is running.

[GenoMax]

Depends what the traitor installer is using. If you are getting that error then it is likely using plain python which would refer to python v.2. Which python does traitar recommend?

[112498262]

In their published paper it says it is implemented in Python 2.7

[GenoMax]

Then I suggest that you look into upgrading your python 2 to the latest version.

[WouterDeCoster]

Yes, but a submodule requires 2.7.9+ or 3.4+. Just upgrade.

[WouterDeCoster]

Biolinux8

I don't know why you picked this one, but you may want to use a more recent operating system.

[112498262]

That's all I have to work with unfortunately.