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author elixir-it
date Thu, 14 Nov 2019 08:54:04 +0000
parents ca1e48c52db9
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#!/bin/bash

cmd="perl \$CONDA_PREFIX/bin/variant_effect_predictor.pl --offline --dir \$CONDA_PREFIX/vep_cache --force_overwrite --species $2 $3 $4 --buffer_size $5 --input_file $6 --output_file $7 --stats_file stat.htm $8"

if [ "$1" == 1 ]; then cmd="$cmd --fork \${GALAXY_SLOTS:-4}"; fi

eval $cmd