diff vep_unico.xml @ 3:ca1e48c52db9 draft

Uploaded

--- a/vep_unico.xml	Thu Oct 25 04:46:04 2018 -0400
+++ b/vep_unico.xml	Sat Sep 21 13:23:01 2019 -0400
@@ -11,27 +11,27 @@
     <requirements>
         <requirement type="package" version="86">variant-effect-predictor</requirement>
 	<requirement type="package" version="1.3.1">samtools</requirement>
-	<requirement type="package" version="1.7.2">perl-bioperl</requirement>
+        <requirement type="package" version="1.0" >openssl</requirement>
     </requirements>
     <command><![CDATA[
 	#if str($veptools.veptoolsselect) =="downloadcache"
 	
-	cd \$CONDA_DEFAULT_ENV && [[ -d vep_cache ]] || mkdir vep_cache ;
+	cd \$CONDA_PREFIX && [[ -d vep_cache ]] || mkdir vep_cache ;
                       cd bin && perl vep_install.pl
                         -a  ac -s $veptools.species
                         --NO_HTSLIB
-                        --CACHEDIR \$CONDA_DEFAULT_ENV/vep_cache;
+                        --CACHEDIR \$CONDA_PREFIX/vep_cache;
                         ## write the cache file downloaded 
                         echo "CACHE DOWNLOADED YET">$output1;
-                        ls \$CONDA_DEFAULT_ENV/vep_cache/*/ >> $output1;
+                        ls \$CONDA_PREFIX/vep_cache/*/ >> $output1;
 	#end if
 
 	
 	#if str($veptools.veptoolsselect) =="annotate"
-	 perl \$CONDA_DEFAULT_ENV/bin/variant_effect_predictor.pl
+	 perl \$CONDA_PREFIX/bin/variant_effect_predictor.pl
         --fork 4
         --offline
-        --dir \$CONDA_DEFAULT_ENV/vep_cache
+        --dir \$CONDA_PREFIX/vep_cache
         --force_overwrite
            #if $veptools.everything.value
            --everything
@@ -54,11 +54,22 @@
             --tumor-id $veptools.tumour_id
             --normal-id $veptools.normal_id
             --buffer-size $veptools.buffer
-            --vep-path \$CONDA_DEFAULT_ENV/bin/
-            --vep-data \$CONDA_DEFAULT_ENV/vep_cache
-            --ref-fasta $veptools.reference
-            --species $veptools.species
-	    --filter-vcf 0 ;
+            --vep-path \$CONDA_PREFIX/bin/
+            --vep-data \$CONDA_PREFIX/vep_cache
+            
+
+
+
+        
+         #if $veptools.reference_source.reference_source_selector == "history"
+         --ref-fasta  $veptools.reference_source.reference
+        #end if
+        #if $veptools.reference_source.reference_source_selector == "cached"
+        --ref-fasta  $veptools.reference_source.ref_file.fields.path
+        #end if
+    
+             --species $veptools.species
+             --filter-vcf 0 ;
 
         #end if
 		 ]]>