# HG changeset patch
# User morinlab
# Date 1485554969 18000
# Node ID a7f44ff74b74195ecf3f02819bc70df269cbd63d
# Parent  651731609448f3ccb1f7aceb3391ea1dfa4726c7
Uploaded

diff -r 651731609448 -r a7f44ff74b74 download_genome.xml
--- a/download_genome.xml	Fri Jan 27 17:06:10 2017 -0500
+++ b/download_genome.xml	Fri Jan 27 17:09:29 2017 -0500
@@ -21,10 +21,11 @@
 	--SPECIES \$(echo $species_select.value | sed 's/-/\t/g' | cut -f1)
 	--CACHEDIR \$ENSEMBL_VEP_84_INSTALL_DIR/cache
 	--CACHEURL ftp://ftp03.bcgsc.ca/public/ensembl/VEP/ --FASTAURL ftp://ftp03.bcgsc.ca/public/ensembl/
-	#if "-" in $species_select.value
-	--ASSEMBLY \$(echo $species_select.value | sed 's/-/\t/g' | cut -f2)
-	                #end if
-	;
+	    #if "-" in $species_select.value
+	    --ASSEMBLY \$(echo $species_select.value | sed 's/-/\t/g' | cut -f2)
+	    #end if
+	    ;
+	#end if
         gzip -d \$ENSEMBL_VEP_84_INSTALL_DIR/cache/\$(echo $species_select.value | sed 's/-/\t/g' | cut -f1 | sed 's/\ /_/g')/*\$(echo $species_select.value | sed 's/-/\t/g' | cut -f2)/*.fa.gz;
       	samtools faidx \$ENSEMBL_VEP_84_INSTALL_DIR/cache/\$(echo $species_select.value | sed 's/-/\t/g' | cut -f1 | sed 's/\ /_/g')/*\$(echo $species_select.value | sed 's/-/\t/g' | cut -f2)/*.fa;