changeset 1:359b0988e735 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_ucsc_tools_0_1 commit 025696892784ba9fd07404ce4d21f3dca4ac1a1e-dirty

--- a/tool_dependencies.xml	Tue May 19 15:03:35 2015 -0400
+++ b/tool_dependencies.xml	Fri Jul 17 14:19:23 2015 -0400
@@ -1,44 +1,30 @@
 <?xml version='1.0' encoding='utf-8'?>
 <tool_dependency>
-    <!-- This package will not track any version of the underlying toools.
-    Any hint how to compile or ship the binaries without violating the license is very much appreciated.
-    -->
     <package name="ucsc_tools" version="0.1">
         <install version="1.0">
-            <actions>
-                <action type="download_binary">
-                    <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
-                    <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
-                    <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
-                    <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template>
-                </action>
-                <action type="chmod">
-                    <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
-                </action>
-                <action type="download_binary">
-                    <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template>
-                    <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
-                    <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
-                    <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
-                </action>
-                <action type="chmod">
-                    <file mode="755">$INSTALL_DIR/bigWigInfo</file>
-                </action>
-                <action type="download_binary">
-                    <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph</url_template>
-                    <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
-                    <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
-                    <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigToBedGraph</url_template>
-                </action>
-                <action type="chmod">
-                    <file mode="755">$INSTALL_DIR/bigWigToBedGraph</file>
-                </action>
+            <actions_group>
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/ucsc/ucsc-312-Linux-x86_64.tar.gz</action>
+                    <action type="shell_command">rm ucsc-312-Linux-x86_64.tar.gz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>
+                </actions>
+                <!--actions architecture="x86_64" os="darwin">
+                    <action type="download_by_url"></action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>
+                </actions-->
                 <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable>
                     <environment_variable name="UCSC_TOOLS_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                 </action>
-             </actions>
+            </actions_group>
          </install>
-         <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
+         <readme>The well known UCSC tools from Jim Kent.</readme>
      </package>
 </tool_dependency>