Mercurial > repos > dereeper > snpeff_from_gff_vcf

comparison 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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0:abde5b0387c8 1:633d264f8888
70 print $C2 "myspecies.genome : myspecies\n"; 70 print $C2 "myspecies.genome : myspecies\n";
71 close($C); 71 close($C);
72 close($C2); 72 close($C2);
73 73
74 74
75 my $build_cmd = "java -jar $SNPEFF_PATH/snpEff.jar build -c $session/snpEff.config -gff3 myspecies"; 75 my $build_cmd = "snpEff build -c $session/snpEff.config -gff3 myspecies";
76 #my $build_cmd = "java -jar $SNPEFF_PATH/snpEff.jar build -c $session/snpEff.config -gff3 myspecies";
76 system($build_cmd); 77 system($build_cmd);
77 78
78 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"; 79 my $eff_cmd = "snpEff eff -c $session/snpEff.config -o vcf -no-downstream -no-upstream myspecies -s $html $input >$output";
80 #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";
79 system($eff_cmd); 81 system($eff_cmd);
80 82
81 83
82 system("rm -rf $session"); 84 system("rm -rf $session");