# HG changeset patch
# User devteam
# Date 1419003057 18000
# Node ID a8f40accd7ceeea58182195bfb905c5d8a815816
# Parent  394b13717223fa2387443c1c93cdd3f875f5531b
Uploaded

diff -r 394b13717223 -r a8f40accd7ce tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Oct 01 12:43:56 2013 -0400
+++ b/tool_dependencies.xml	Fri Dec 19 10:30:57 2014 -0500
@@ -3,15 +3,15 @@
     <package name="cufflinks" version="2.1.1">
         <install version="1.0">
             <actions_group>
-                <actions os="linux" architecture="x86_64">
-                    <action type="download_by_url">http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.1.1.Linux_x86_64.tar.gz</action>
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url">http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.1.1.Linux_x86_64.tar.gz</action>
                     <action type="move_directory_files">
                         <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR/bin</destination_directory>
                     </action>
                 </actions>
-                <actions os="darwin" architecture="x86_64">
-                    <action type="download_by_url">http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.1.1.OSX_x86_64.tar.gz</action>
+                <actions architecture="x86_64" os="darwin">
+                    <action type="download_by_url">http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.1.1.OSX_x86_64.tar.gz</action>
                     <action type="move_directory_files">
                         <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR/bin</destination_directory>
@@ -19,23 +19,23 @@
                 </actions>
                 <actions>
                     <package name="boost" version="1.53.0">
-                        <repository changeset_revision="dbdde1a2d0c5" name="package_boost_1_53" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu/"  prior_installation_required="True" />
+                        <repository changeset_revision="cee17eb9de41" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                     </package>
                     <package name="samtools" version="0.1.18">
-                        <repository changeset_revision="171cd8bc208d"  name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu/"  prior_installation_required="True" />
+                        <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                     </package>
                     <package name="eigen" version="3.2.0">
-                        <repository changeset_revision="c6204ba02233" name="package_eigen_3_2_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu/"  prior_installation_required="True" />
+                        <repository changeset_revision="c6204ba02233" name="package_eigen_3_2_0" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                     </package>
                     <action type="download_by_url">http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.1.1.tar.gz</action>
                     <action type="set_environment_for_install">
-                        <repository changeset_revision="dbdde1a2d0c5" name="package_boost_1_53" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu/"  prior_installation_required="True">
+                        <repository changeset_revision="cee17eb9de41" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                             <package name="boost" version="1.53.0" />
                         </repository>
-                        <repository changeset_revision="171cd8bc208d"  name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu/"  prior_installation_required="True">
+                        <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                             <package name="samtools" version="0.1.18" />
                         </repository>
-                        <repository changeset_revision="c6204ba02233" name="package_eigen_3_2_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu/"  prior_installation_required="True">
+                        <repository changeset_revision="c6204ba02233" name="package_eigen_3_2_0" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                             <package name="eigen" version="3.2.0" />
                         </repository>
                     </action>
@@ -43,10 +43,10 @@
                     <action type="shell_command">make &amp;&amp; make install</action>
                 </actions>
                 <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                 </action>
             </actions_group>
         </install>
-        <readme></readme>
+        <readme />
     </package>
 </tool_dependency>