Mercurial > repos > elixir-it > vep86_vcf2maf

diff vep_unico.sh @ 3:ca1e48c52db9 draft

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author elixir-it
date Sat, 21 Sep 2019 13:23:01 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vep_unico.sh	Sat Sep 21 13:23:01 2019 -0400
@@ -0,0 +1,9 @@
+#!/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
+
+