# HG changeset patch
# User morinlab
# Date 1485466594 18000
# Node ID 08f70fb169d088ae7903af7373fe098692dc398e
# Parent  c035dd918ed44c74806225359035517e02d04403
Uploaded

diff -r c035dd918ed4 -r 08f70fb169d0 tool_dependencies.xml
--- a/tool_dependencies.xml	Sat Dec 03 18:59:25 2016 -0500
+++ b/tool_dependencies.xml	Thu Jan 26 16:36:34 2017 -0500
@@ -15,7 +15,7 @@
                           <package name="ensembl_vep_perl_env" version="84" />
                      </repository>
                 </action>
-		<action type="shell_command">mkdir $INSTALL_DIR/cache</action>
+<action type="shell_command">mkdir $INSTALL_DIR/cache</action>
                 <action type="shell_command">mkdir $INSTALL_DIR/cache/tmp</action>
                 <action type="shell_command">chmod 777 $INSTALL_DIR/cache</action>
                 <action type="shell_command">chmod 777 $INSTALL_DIR/cache/tmp</action>
@@ -24,8 +24,10 @@
                     <destination_directory>$INSTALL_DIR</destination_directory>
                 </action>
                 <action type="set_environment">
-                    <environment_variable action="set_to" name="ENSEMBL_VEP_84_INSTALL_DIR">$INSTALL_DIR</environment_variable>
-                    <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/Bio</environment_variable>
+                  <environment_variable action="set_to" name="ENSEMBL_VEP_84_INSTALL_DIR">$INSTALL_DIR</environment_variable>
+		  <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/Bio</environment_variable>
+                  <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR</environment_variable>
+		  <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/htslib</environment_variable>
                 </action>
                 <action type="shell_command">echo 'y' | perl $INSTALL_DIR/INSTALL.pl --DESTDIR $INSTALL_DIR -q --AUTO a</action>
             </actions>