wangdi2014

## simple_args_parsing.sh
#!/bin/sh

#
# a simple way to parse shell script arguments
#
# please edit and use to your hearts content
#


ENVIRONMENT="dev"

## ensembl_vep_102_with_offline_cache.md

      
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                wangdi2014
                / ensembl_vep_102_with_offline_cache.md
            
            
              Created
              April 21, 2021 15:18
                — forked from ckandoth/ensembl_vep_102_with_offline_cache.md
            
              
                Install Ensembl's VEP v102 with local cache for running offline
              
          
    Ensembl's VEP (Variant Effect Predictor) is popular for how it picks a single effect per gene as detailed here, its CLIA-compliant HGVS variant format, and Sequence Ontology nomenclature for variant effects.
Instead of the official instructions, we will use conda to install VEP and its dependencies. If you don't already have conda, install it into $HOME/miniconda3 as follows:
curl -sL https://repo.anaconda.com/miniconda/Miniconda3-py37_4.9.2-Linux-x86_64.sh -o /tmp/miniconda.sh
sh /tmp/miniconda.sh -bfp $HOME/miniconda3
Add the conda bin folder into your $PATH so that all installed tools are accessible via command-line. You can also add this to your ~/.bashrc
	#!/bin/sh

	#
	# a simple way to parse shell script arguments
	#
	# please edit and use to your hearts content
	#


	ENVIRONMENT="dev"