search

wodanaz / Assembling_viruses

0 stars 0 forks source link

Prevent malware warning for pillow #81

Open johnbradley opened 2 years ago

johnbradley commented 2 years ago

We received a warning that there was malware in the conda environment created for running the pipeline. The problematic file was .conda/pkgs/pillow-9.0.0-py310h2f95282_0/info/recipe/Tests/images/crash-81154a65438ba5aaeca73fd502fa4850fbde60f8.tif. This looks to be an example bad file that was used to test pillow and not actually malware. It looks like the image that causes malware detection problems was removed by https://github.com/python-pillow/Pillow/pull/5561.

Perhaps we can just regenerate conda environments to resolve this problem.

johnbradley commented 2 years ago

I tested with a new conda environment and this file is still installed when installing the snakemake environment for running the pipeline from the pillow 9.0.1 conda package. The bad file was removed from the main pillow repository, but added to the pillow-feedstock: https://github.com/conda-forge/pillow-feedstock/commit/6ae34ee4023f5365fb33660e7454eb34ec66c508

I was able to install snakemake with an older version of pillow like so:

conda create -n snakemake -c conda-forge -c bioconda mamba snakemake==6.4.1 pillow=8.4.0
johnbradley commented 2 years ago

I commented on an issue in the pillow-feedstock about this problem: https://github.com/conda-forge/pillow-feedstock/issues/113#issuecomment-1065480082