added VEP plugin repo and faatpipe repo to config and setup.sh file

PMBio · Oct 9, 2023 · c3347c1 · c3347c1
1 parent a5125a8
commit c3347c1
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diff --git a/deeprvat/annotations/setup_annotation_workflow.sh b/deeprvat/annotations/setup_annotation_workflow.sh
@@ -35,6 +35,9 @@ echo "- DeepRiPe(faatpipe)"
 mkdir -p $REPO_DIR/faatpipe
 git clone https://github.com/HealthML/faatpipe.git $REPO_DIR/faatpipe
 
+echo vep plugins
+mkdir -p $REPO_DIR/VEP_plugins
+git clone https://github.com/Ensembl/VEP_plugins.git $REPO_DIR/VEP_plugins
 ##returning to main environment
 
 mamba activate deeprvat_annotations

diff --git a/pipelines/config/deeprvat_annotation_config.yaml b/pipelines/config/deeprvat_annotation_config.yaml
@@ -24,7 +24,9 @@ cadd_indel_file : annotation_data/cadd/gnomad.genomes.r3.0.indel.tsv.gz
 absplice_repo_dir : repo_dir/absplice
 deeprvat_repo_dir : deeprvat_repo_dir
 kipoiveff_repo_dir : repo_dir/kipoi-veff2
+faatpipe_repo_dir : repo_dir/faatpipe
 vep_repo_dir : repo_dir/ensembl-vep
+vep_plugin_repo : repo_dir/VEP_plugins
 variant_file_path : preprocessing_workdir/norm/variants/variants.tsv.gz
 pybedtools_tmp_path : output_dir/annotations/tmp/pybedtools
 n_jobs_deepripe : 32