Cannot solve conda environment

[hgrandjean]

Dear @durrantmm ,

Just got to the realm of MGE identification and was very interested in your tool and approach.
Sadly, i'v tried installing MGEfinder on both mac and linux with conda, mamba and miniconda using strict chanel priority,.
All 3 return the same error as follow :

Removing mgefinder environment if already installed...

EnvironmentLocationNotFound: Not a conda environment: /Users/path/miniconda3/envs/mgefinder

Installing mgefinder environment...
Channels:
 - bioconda
 - defaults
 - conda-forge
 - r
Platform: osx-64
Collecting package metadata (repodata.json): done
Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - package libffi-3.2.1-h475c297_4 is excluded by strict repo priority
  - package pynacl-1.3.0-py36h1de35cc_0 is excluded by strict repo priority
  - package urllib3-1.25.7-py36_0 is excluded by strict repo priority

I finally succeeded using flexible priority (which i'm not confident with for version reliability).

I noticed the yaml files you kindly provided presents both versioning and build hashes for the different packages.
Would you be able to tell which packages version are influencing results obtained by MGEfinder and which could be let free of version control ?

Here is a proposed list of packages that i assumed would be important to lock version for results reproducibility, id be happy to revise it with your comments.

Proposed list with importance for version control

• bwa
• cd-hit
• emboss
• htslib
• pysam
• samtools
• numpy/numpy-base
• pandas
• scipy
• biopython
• networkx
• mkl/mkl_fft/mkl_random
• blas
• snakemake
• python
• perl

Thank you in advance for you time and help,

Best regards,
H