Strict requirements for old version of numpy?

[russellsmithies]

We're having problems with the strict requirement for an old version of numpy ('numpy<1.12.0,>=1.11.0' ) that prevents many other applications running (eg srst2, snapperdb etc). Do you actually need such an old version of numpy or could you manage with the current? The alternative is we stop using PHEnix :-(

[tseemann]

Russel, i am not an author of PHEnix but you have a few options.

1. Use virtualenv, pyenv etc to have separate environments for each big app

2. After you git clone PHEnix, just edit the requirements.txt file and change the numpy line. eg. https://github.com/phe-bioinformatics/PHEnix/blob/master/requirements.txt and see if it works!

3. Try an alternative SNP caller, for example

• snippy https://github.com/tseemann/snippy (my tool)
• nasp
• snp-pipeline

[Wang-Jing-NZ]

Thank you, Torsten, for your reply. I will try to snippy and GATK outputs first.

Cheers
Jing

[ulfschaefer]

Before you abandon the goodness that is PHEnix for brighter shores ...

This is a case of not tidying up. The requirement for numpy can be removed. The code used to call mean and std from numpy, but it does not appear to do so any more.

68d35c2

And sorry for the late reply. Let me know if you have any problems with this. I will reply faster now.

[russellsmithies]

All sorted now I think, we'll do a bit more testing to confirm :-)