https://github.com/sanger-pathogens/gubbins
Tip revision: 21e70def99edad2d47c150c3ed291ad11350a2d3 authored by Nick Croucher on 05 May 2023, 07:14:44 UTC
Update to use SKA2
Update to use SKA2
Tip revision: 21e70de
environment.yml
name: gubbins_env
channels:
- conda-forge
- bioconda
- defaults
- r
dependencies:
# python
- python>=3.8
# installation
- autoconf
- automake
- autoconf-archive
- pytest
- pytest-cov
- lcov
- check
- libtool
- cppunit
- pkg-config
- wheel
- pillow
# algorithm
- scipy
- dendropy
- biopython
- multiprocess
- numpy<=1.23.0
- numba
# phylogenetics
- raxml=8.2.12
- iqtree>=2.2
- rapidnj
- raxml-ng=1.0.1
- fasttree=2.1.10
# Scripts
- ska2