# HG changeset patch
# User iracooke
# Date 1394515761 14400
# Node ID d21f91402d1cd19455796e3fee686c4d5b4fc806
# Parent  b2d5b8844b5c09d1012ffc096d5c8338d20ad461
Uploaded

diff -r b2d5b8844b5c -r d21f91402d1c tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Mar 10 22:17:16 2014 -0400
+++ b/tool_dependencies.xml	Tue Mar 11 01:29:21 2014 -0400
@@ -7,6 +7,7 @@
 				<url_template os="linux">https://dl.dropboxusercontent.com/u/226794/galaxy/pwiz-bin-linux-x86_64-gcc42-release-3_0_4388/chainsaw</url_template>
         <url_template os="linux">https://dl.dropboxusercontent.com/u/226794/galaxy/pwiz-bin-darwin-x86-xgcc40-release-3_0_4388/chainsaw</url_template>
       </action>
+
       <action type="download_binary">
         <url_template os="linux">https://dl.dropboxusercontent.com/u/226794/galaxy/pwiz-bin-linux-x86_64-gcc42-release-3_0_4388/idcat</url_template>
         <url_template os="linux">https://dl.dropboxusercontent.com/u/226794/galaxy/pwiz-bin-darwin-x86-xgcc40-release-3_0_4388/idcat</url_template>
@@ -15,9 +16,6 @@
         <url_template os="linux">https://dl.dropboxusercontent.com/u/226794/galaxy/pwiz-bin-linux-x86_64-gcc42-release-3_0_4388/idconvert</url_template>
         <url_template os="linux">https://dl.dropboxusercontent.com/u/226794/galaxy/pwiz-bin-darwin-x86-xgcc40-release-3_0_4388/idconvert</url_template>
       </action>
-      <action type="shell_command">
-        chmod u+x $INSTALL_DIR/idconvert; echo $INSTALL_DIR
-      </action>
       <action type="download_binary">
         <url_template os="linux">https://dl.dropboxusercontent.com/u/226794/galaxy/pwiz-bin-linux-x86_64-gcc42-release-3_0_4388/license</url_template>
         <url_template os="linux">https://dl.dropboxusercontent.com/u/226794/galaxy/pwiz-bin-darwin-x86-xgcc40-release-3_0_4388/license</url_template>
@@ -77,8 +75,23 @@
         <url_template os="linux">https://dl.dropboxusercontent.com/u/226794/galaxy/pwiz-bin-darwin-x86-xgcc40-release-3_0_4388/unimod_2.xsd</url_template>
       </action>
       
-      <action type="shell_command">
-        chmod ug+x $INSTALL_DIR/chainsaw $INSTALL_DIR/idcat $INSTALL_DIR/idconvert $INSTALL_DIR/msaccess $INSTALL_DIR/msbenchmark $INSTALL_DIR/mscat $INSTALL_DIR/msconvert $INSTALL_DIR/msdiff $INSTALL_DIR/msdir $INSTALL_DIR/msistats $INSTALL_DIR/mspicture $INSTALL_DIR/peakaboo $INSTALL_DIR/pepcat $INSTALL_DIR/pepsum $INSTALL_DIR/sldout $INSTALL_DIR/txt2mzml
+      <action type="chmod">
+        <file mode="750">$INSTALL_DIR/chainsaw</file>
+        <file mode="750">$INSTALL_DIR/idcat</file>
+        <file mode="750">$INSTALL_DIR/idconvert</file>
+        <file mode="750">$INSTALL_DIR/msaccess</file>
+        <file mode="750">$INSTALL_DIR/msbenchmark</file>
+        <file mode="750">$INSTALL_DIR/mscat</file>                
+        <file mode="750">$INSTALL_DIR/msconvert</file>
+        <file mode="750">$INSTALL_DIR/msdiff</file>
+        <file mode="750">$INSTALL_DIR/msdir</file>
+        <file mode="750">$INSTALL_DIR/msistats</file>
+        <file mode="750">$INSTALL_DIR/mspicture</file>
+        <file mode="750">$INSTALL_DIR/peakaboo</file>
+        <file mode="750">$INSTALL_DIR/pepcat</file>
+        <file mode="750">$INSTALL_DIR/pepsum</file>
+        <file mode="750">$INSTALL_DIR/sldout</file>
+        <file mode="750">$INSTALL_DIR/txt2mzml</file>        
       </action>
 
           <action type="set_environment">