install_openCravat.md

OpenCravat

Original documentation for OpenCravat can be found here.

Installation

Create conda environment

# create conda environment. Needed only the first time.
conda create -n opencravat

# activate environment
conda activate opencravat

Install openCravat

pip3 install open-cravat==2.4.1

Set Modules Directory

Use oc config md to see where modules directory is currently pointed to. To change the modules directory, use oc config md [new directory] to point OpencRAVAT to the new directory.

Test it by using oc config md command. It should output the new modules directory.

Install necessary modules for DITTO

oc module install-base

oc module  install aloft cadd cadd_exome cancer_genome_interpreter ccre_screen chasmplus civic clingen clinpred clinvar \
cosmic cosmic_gene cscape dann dann_coding dbscsnv dbsnp dgi ensembl_regulatory_build ess_gene exac_gene fathmm \
fathmm_xf_coding funseq2 genehancer gerp ghis gnomad gnomad3 gnomad_gene gtex gwas_catalog linsight loftool lrt mavedb \
metalr metasvm mutation_assessor mutationtaster mutpred1 mutpred_indel ncbigene ndex ndex_chd ndex_signor omim \
pangalodb phastcons phdsnpg phi phylop polyphen2 prec provean repeat revel rvis segway sift siphy spliceai uniprot \
vest cgc cgd varity_r

Please look at the install logs for the versions of all the above annotators used to train the current DITTO model.

Install reporter modules for DITTO

List available reporters

oc module ls -a -t reporter

Install reporters

oc module install vcfreporter csvreporter tsvreporter -y

Setup modules package for DITTO pipeline

Package is a module which defines module installation and job parameters. To learn more about OpenCravat's package, please click here.

Here's the package for DITTO - configs/mypackage/mypackage.yml

Copy the package directory to the modules directory.

# Use this to check the modules directory
oc config md

# copy the package to the modules directory
cp -r configs/mypackage path/to/modules/directory/