changeset 1:5821ea743daf draft

planemo upload commit d7c267cd350a630f61aaf721b32c2f913d04c9d4

--- a/tool_dependencies.xml	Tue May 16 15:18:16 2017 -0400
+++ b/tool_dependencies.xml	Wed May 17 12:40:14 2017 -0400
@@ -1,57 +1,29 @@
 <?xml version="1.0" ?>
 <tool_dependency>
-    <package name="ucsc_twobit" version="340">
+    <package name="ucsc_hac" version="340">
         <install version="1.0">
             <actions_group>
-                <actions os="darwin" architecture="x86_64">
-                    <action type="download_by_url"
-                            sha256sum="aa0df6fc9c5dfe83cb94456e1100a5ecd7a247e7521d91f4e91c46c1b21fc9ab">
-                        http://old-gep.wustl.edu/~wilson/packages/ucsc_twobit/ucsc_twobit_340_macOS_x86_64.tar.gz
-                    </action>
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/ucsc_tools_340.tar.gz</action>
                     <action type="move_directory_files">
-                        <source_directory>bin</source_directory>
+                        <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR/bin</destination_directory>
                     </action>
                 </actions>
-
-                <actions os="linux" architecture="x86_64">
-                    <action type="download_by_url"
-                            sha256sum="31b18fd6f0f24981815ded0a1790be49ca47a5d2cce40c3af29ffc6f5bea4922">
-                        http://old-gep.wustl.edu/~wilson/packages/ucsc_twobit/ucsc_twobit_340_linux_x86_64.tar.gz
-                    </action>
-                    <action type="move_directory_files">
-                        <source_directory>bin</source_directory>
-                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
-                    </action>
-                </actions>
-
-                <!-- Display error message for unsupported OS and CPU architecture -->
-                <actions>
-                    <action type="shell_command">
-                        echo "ERROR: This package only supports 64-bit systems running macOS or Linux"
-                    </action>
-                    <action type="shell_command">false</action>
-                </actions>
-
-                <!-- update $PATH environment variable -->
                 <action type="set_environment">
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                 </action>
             </actions_group>
-        </install>
-        <readme>
-        <![CDATA[
-            This package contains the utilities for constructing and manipulating
-            `twoBit files <https://genome.ucsc.edu/goldenpath/help/twoBit.html>`_.
-            The utilities were created by the
-            `Genome Bioinformatics Group <https://genome.ucsc.edu/staff.html>`_
-            at the UCSC Genomics Institute.
-
-            The twoBit file format is designed to store genomic sequences and the
-            associated repeat masking information. The twoBit file is used by the
-            UCSC Genome Browser and by tools such as
-            `BLAT <https://genome.ucsc.edu/goldenpath/help/blatSpec.html>`_.
-        ]]>
-        </readme>
+         </install>
+         <readme>The well known UCSC tools from Jim Kent. This subset of UCSC tools are used for HubArchiveCreator, including 
+         - bedGraphToBigWig
+         - bedToBigBed
+         - gff3ToGenePred
+         - gtfToGenePred
+         - genePredToBed
+         - genePredToBigGenePred
+         - faToTwoBit
+         - pslToBigPsl
+         </readme>
     </package>
 </tool_dependency>