cnv_prep.md

CNV GATK env prep

Prep gatk env:

You can choose one of those options:

1. create gatk env and use it while runnig the "CNVworkflow”:

   cd workflow/env
   mamba env create -n gatk -f gatkcondaenv.yml

2. update current env with required packages (not recommended):

   cd workflow/env
   conda env update --file gatkcondaenv.yml --name wes_gatk --prune

3. to update Python env only (not recommended):

   pip install workflow/env/gatkPythonPackageArchive.zip

To check install is successful

run:

conda activate gatk # or wes_gatk if you updated this env 
conda list 

You should find gatkpythonpackages in the packages list

you can also test the python required package as follows:

conda activate gatk # or wes_gatk if you updated this env 
python -c "import gcnvkernel"

it should run without any errors

Some troubleshooting:

if you face this error ModuleNotFoundError: No module named 'numpy.testing.decorators' you can try the solution posted in this post: https://gatk.broadinstitute.org/hc/en-us/community/posts/360056743551-Problem-Installing-GATK-python-environment-SOLUTION-POSTED-

or this video: https://www.youtube.com/watch?v=je5iskPlNkg&ab_channel=Sky'sBioinformatics