Mercurial > repos > dereeper > snpeff_from_gff_vcf

diff SnpEff.pl @ 1:633d264f8888 draft default tip

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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
author dereeper
date Mon, 16 Apr 2018 08:56:29 -0400
parents abde5b0387c8
children
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line diff
--- a/SnpEff.pl	Mon Mar 23 05:17:19 2015 -0400
+++ b/SnpEff.pl	Mon Apr 16 08:56:29 2018 -0400
@@ -72,10 +72,12 @@
 close($C2);
 
 
-my $build_cmd = "java -jar $SNPEFF_PATH/snpEff.jar build -c $session/snpEff.config -gff3 myspecies";
+my $build_cmd = "snpEff build -c $session/snpEff.config -gff3 myspecies";
+#my $build_cmd = "java -jar $SNPEFF_PATH/snpEff.jar build -c $session/snpEff.config -gff3 myspecies";
 system($build_cmd);
 
-my $eff_cmd = "java -jar $SNPEFF_PATH/snpEff.jar eff -c $session/snpEff.config -o vcf -no-downstream -no-upstream myspecies -s $html $input >$output";
+my $eff_cmd = "snpEff eff -c $session/snpEff.config -o vcf -no-downstream -no-upstream myspecies -s $html $input >$output";
+#my $eff_cmd = "java -jar $SNPEFF_PATH/snpEff.jar eff -c $session/snpEff.config -o vcf -no-downstream -no-upstream myspecies -s $html $input >$output";
 system($eff_cmd);