Mercurial > repos > dvanzessen > pvac_seq_emc

diff pvac-seq.xml @ 3:409392edf036 draft

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Uploaded
author dvanzessen
date Wed, 17 Jul 2019 08:43:23 -0400
parents b5859fc0342d
children 2ae8171ba4d9
line wrap: on
line diff
--- a/pvac-seq.xml	Wed Jul 17 08:03:29 2019 -0400
+++ b/pvac-seq.xml	Wed Jul 17 08:43:23 2019 -0400
@@ -1,7 +1,4 @@
 <tool id="pvac-seq" name="PVAC-seq" version="0.1.0">
-    <environment_variables>
-        <environment_variable name="IEDB_INSTALL_DIRECTORY">$IEDB_INSTALL_DIRECTORY</environment_variable>
-    </environment_variables>
     <command detect_errors="exit_code"><![CDATA[
         #if str( $epitope_length ) != "":
             #set $epitope_length = "-e " + str($epitope_length)
@@ -9,7 +6,7 @@
         #set algs = ' '.join([str($alg) for $alg in $algorithms]) 
         pvacseq run 
         ${epitope_length} 
-        --iedb-install-directory $IEDB_INSTALL_DIRECTORY
+        --iedb-install-directory "\$IEDB_INSTALL_DIRECTORY"
         --tdna-vaf ${tdna_vaf} 
         --net-chop-method ${net_chop_method} 
         ${net_mhc_stab}