# HG changeset patch
# User devteam
# Date 1450481814 18000
# Node ID a8a50dd7f5c672b3dd141978ab58fd298176f4cf
# Parent  1b08f4e805092244764f88c057dfacb642a2f1c6
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_cufflinks_2_1_1 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6

diff -r 1b08f4e80509 -r a8a50dd7f5c6 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Oct 01 10:57:19 2013 -0400
+++ b/tool_dependencies.xml	Fri Dec 18 18:36:54 2015 -0500
@@ -4,42 +4,42 @@
         <install version="1.0">
             <actions_group>
                 <actions architecture="x86_64" os="linux">
-                    <action type="download_by_url">http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.1.1.Linux_x86_64.tar.gz</action>
+                    <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>$INSTALL_DIR/bin</destination_directory>
                     </action>
                 </actions>
                 <actions architecture="x86_64" os="darwin">
-                    <action type="download_by_url">http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.1.1.OSX_x86_64.tar.gz</action>
+                    <action type="download_by_url">http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.1.1.OSX_x86_64.tar.gz</action>
                     <action type="move_directory_files">
                         <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR/bin</destination_directory>
                     </action>
                 </actions>
                 <actions>
-                    <package name="boost" version="1.54.0">
-                        <repository changeset_revision="0464d82a4c3f" name="package_boost_1_54" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+                    <package name="boost" version="1.53.0">
+                        <repository changeset_revision="a534981960ca" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                     </package>
                     <package name="samtools" version="0.1.18">
-                        <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+                        <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                     </package>
                     <package name="eigen" version="3.2.0">
-                        <repository changeset_revision="dfd2503afe0d" name="package_eigen_3_2_0" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+                        <repository changeset_revision="dfd2503afe0d" name="package_eigen_3_2_0" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.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="download_by_url">http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.1.1.tar.gz</action>
                     <action type="set_environment_for_install">
-                        <repository changeset_revision="0464d82a4c3f" name="package_boost_1_54" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                            <package name="boost" version="1.54.0" />
+                        <repository changeset_revision="a534981960ca" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                            <package name="boost" version="1.53.0" />
                         </repository>
-                        <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                             <package name="samtools" version="0.1.18" />
                         </repository>
-                        <repository changeset_revision="dfd2503afe0d" name="package_eigen_3_2_0" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <repository changeset_revision="dfd2503afe0d" name="package_eigen_3_2_0" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                             <package name="eigen" version="3.2.0" />
                         </repository>
                     </action>
-                    <action type="shell_command">./configure --prefix=$INSTALL_DIR --with-boost=$BOOST_ROOT --with-bam=$BAM_ROOT --with-eigen=$EIGEN_ROOT</action>
+                    <action type="shell_command">./configure --prefix=$INSTALL_DIR --with-boost=$BOOST_ROOT_DIR --with-bam=$BAM_ROOT --with-eigen=$EIGEN_ROOT</action>
                     <action type="shell_command">make &amp;&amp; make install</action>
                 </actions>
                 <action type="set_environment">