diff tool_dependencies.xml @ 5:fb4104623d3f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit 0347bb0b05cae8686a0c2a51285a80f0dffc3b54

--- a/tool_dependencies.xml	Mon Jun 01 22:50:24 2015 -0400
+++ b/tool_dependencies.xml	Fri Jun 26 13:22:54 2015 -0400
@@ -9,13 +9,6 @@
     <package name="samtools" version="1.2">
         <install version="1.0">
             <actions_group>
-                <actions architecture="x86_64" os="linux">
-                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-1.2-Linux-x86_64.tgz</action>
-                    <action type="move_directory_files">
-                        <source_directory>.</source_directory>
-                        <destination_directory>$INSTALL_DIR</destination_directory>
-                    </action>
-                </actions>
                 <actions>
                     <action type="download_by_url">https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2</action>
                     <action type="set_environment_for_install">
@@ -34,6 +27,15 @@
                         <source>samtools</source>
                         <destination>$INSTALL_DIR/bin</destination>
                     </action>
+                    <action type="shell_command">cd htslib-1.2.1 &amp;&amp; make bgzip tabix</action>
+                    <action type="move_file">
+                        <source>bgzip</source>
+                        <destination>$INSTALL_DIR/bin</destination>
+                    </action>
+                    <action type="move_file">
+                        <source>tabix</source>
+                        <destination>$INSTALL_DIR/bin</destination>
+                    </action>
                 </actions>
                 <action type="set_environment">
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>