# HG changeset patch
# User morinlab
# Date 1485556656 18000
# Node ID 9c48b6d4b110630dfde932ef5661adaf4e0bccb0
# Parent  56d99be4cc8f126e767438830eb918b42c0641c2
Deleted selected files

diff -r 56d99be4cc8f -r 9c48b6d4b110 download_genome.xml
--- a/download_genome.xml	Fri Jan 27 17:36:09 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,48 +0,0 @@
-<tool id="download_genome" name="Get Genome" version="1.0.0">
-    <description>
-      Download and Index Genomes and Reference files used by Ensemble VEP
-    </description>
-    <requirements>
-        <requirement type="package" version="84">ensembl_vep</requirement>
-    </requirements>    
-    <command>
-      #if $use_mirror.value == "no":
-	perl \$ENSEMBL_VEP_84_INSTALL_DIR/INSTALL.pl 
-		--AUTO cf 
-		--SPECIES \$(echo $species_select.value | sed 's/-/\t/g' | cut -f1) 
-		--CACHEDIR \$ENSEMBL_VEP_84_INSTALL_DIR/cache
-		#if "-" in $species_select.value
-		  --ASSEMBLY \$(echo $species_select.value | sed 's/-/\t/g' | cut -f2)
-		#end if
-        ;
-        #else:
-	perl \$ENSEMBL_VEP_84_INSTALL_DIR/INSTALL.pl
-	--AUTO cf
-	--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
-	    ;
-	#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;
-	
-	env > $output;
-   </command>
-    <inputs>
-      <expand macro="genome_list" />
-      <param name="use_mirror" type="boolean" checked="false" label="use North American mirror site for download" display="radio" truevalue="yes" falsevalue="no"/>
-    </inputs>
-    <outputs>
-        <data format="txt" name="output"/>
-    </outputs>
-    <stdio>
-        <exit_code range="1:" level="fatal" description="Failure" />
-    </stdio>
-    <macros>
-      <import>ensembl_vep_macros.xml</import>
-    </macros>
-    
-</tool>