diff tool_dependencies.xml @ 55:ba9997c847dc draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty

--- a/tool_dependencies.xml	Tue May 16 18:09:00 2017 -0400
+++ b/tool_dependencies.xml	Wed May 17 13:16:57 2017 -0400
@@ -1,6 +1,5 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <!-- UCSC Tools in  -->
     <!-- Useful for HAC are:
         - twoBitInfo
         - sort
@@ -16,75 +15,15 @@
     <package name="samtools" version="1.2">
         <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-
-    <package name="ucsc_tools_340" version="1.0">
-        <install version="1.0">
-            <actions_group>
-                <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>.</source_directory>
-                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
-                    </action>
-                </actions>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions_group>
-         </install>
-         <readme>The well known UCSC tools from Jim Kent.</readme>
+    <package name="ucsc_hac" version="340">
+        <repository changeset_revision="1368b25a0ae0" name="package_ucsc_hac_340" owner="yating-l" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="ucsc_bigbed" version="340">
+        <repository changeset_revision="dd9b230c079d" name="package_ucsc_bigbed_340" owner="yating-l" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 
-    <!-- package ucsc_bigwig is created by Wilson Leung -->
-    <package name="ucsc_bigwig" version="340">
-        <install version="1.0">
-            <actions_group>
-                <actions architecture="x86_64" os="darwin">
-                    <action sha256sum="a34c57a9fb3c36a984b8fa879a99697c994cd981a1277663d372638e4dec8bb2" type="download_by_url">
-                        http://old-gep.wustl.edu/~wilson/packages/ucsc_bigwig/ucsc_bigwig_340_macOS_x86_64.tar.gz
-                    </action>
-                    <action type="move_directory_files">
-                        <source_directory>bin</source_directory>
-                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
-                    </action>
-                </actions>
-
-                <actions architecture="x86_64" os="linux">
-                    <action sha256sum="0d2bd886e312980e0ae58ae912315beeeac612fd1783c959b4eabd62cffd8512" type="download_by_url">
-                        http://old-gep.wustl.edu/~wilson/packages/ucsc_bigwig/ucsc_bigwig_340_linux_x86_64.tar.gz
-                    </action>
-                    <action type="move_directory_files">
-                        <source_directory>bin</source_directory>
-                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
-                    </action>
-                </actions>
+    <package name="ucsc_bigwig" version="340">      
+        <repository changeset_revision="06411298fa7d" name="package_ucsc_bigwig_340" owner="yating-l" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
 
-                <!-- 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 $PATH environment variable -->
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions_group>
-        </install>
-        <readme>
-        
-            This package contains the utilities for constructing
-            `bigWig files &lt;https://genome.ucsc.edu/goldenpath/help/bigWig.html&gt;`_.
-            The utilities were created by the
-            `Genome Bioinformatics Group &lt;https://genome.ucsc.edu/staff.html&gt;`_
-            at the UCSC Genomics Institute.
-
-            The bigWig file format is designed to store dense continuous datasets
-            and it is compatible with many genome browsers (e.g., UCSC Genome Browser,
-            JBrowse, IGV).
-        
-        </readme>
-    </package>
 </tool_dependency>