From 3388417063053a4c0b51b7edfb657540496301e8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C3=BCck?= Date: Fri, 24 May 2024 16:20:22 +0200 Subject: [PATCH] updated setup shell script for annotations --- deeprvat/annotations/setup_annotation_workflow.sh | 9 --------- 1 file changed, 9 deletions(-) diff --git a/deeprvat/annotations/setup_annotation_workflow.sh b/deeprvat/annotations/setup_annotation_workflow.sh index 76ba0d13..cf0ea93b 100644 --- a/deeprvat/annotations/setup_annotation_workflow.sh +++ b/deeprvat/annotations/setup_annotation_workflow.sh @@ -13,15 +13,6 @@ git checkout release/111 perl INSTALL.pl --AUTO acfp --ASSEMBLY GRCh38 --CACHEDIR $VEP_CACHEDIR --PLUGINS CADD, SpliceAI, PrimateAI --PLUGINSDIR $VEP_PLUGINDIR --species homo_sapiens cd ../.. -echo "- AbSplice" -mkdir -p $REPO_DIR/absplice -git clone https://github.com/gagneurlab/absplice.git $REPO_DIR/absplice -cd $REPO_DIR/absplice -mamba env create -f environment.yaml -mamba activate absplice -pip install -e . -cd ../.. - echo "- DeepSea(kipoi-veff2)" mkdir -p $REPO_DIR/kipoi-veff2 git clone https://github.com/kipoi/kipoi-veff2.git $REPO_DIR/kipoi-veff2