diff tool_dependencies.xml @ 0:06cb587a5e87 draft

Uploaded initial version 2.1.0-4.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Jun 30 08:16:18 2015 -0400
@@ -0,0 +1,65 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <!-- Dependencies from main/test toolsheds -->
+  <package name="numpy" version="1.9">
+    <repository changeset_revision="84e97f5cd3ab" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="R" version="3.1.2">
+    <repository changeset_revision="6e0eee4ea4e1" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+  <!-- Subset of UCSC tools -->
+  <package name="ucsc_tools_for_macs21" version="1.0">
+      <install version="1.0">
+            <actions>
+	      <!-- fetchChromSizes -->
+              <action type="download_binary">
+                <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes</url_template>
+              </action>
+              <action type="chmod">
+                <file mode="755">$INSTALL_DIR/fetchChromSizes</file>
+              </action>
+	      <!-- bedClip -->
+              <action type="download_binary">
+                <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedClip</url_template>
+              </action>
+              <action type="chmod">
+                <file mode="755">$INSTALL_DIR/bedClip</file>
+              </action>
+	      <!-- bedGraphToBigWig -->
+              <action type="download_binary">
+                <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
+              </action>
+              <action type="chmod">
+                <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
+              </action>
+              <action type="set_environment">
+                <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
+              </action>
+	    </actions>
+      </install>
+  </package>
+  <!-- MACS 2.1.0 -->
+  <package name="macs2" version="2.1.0.20140616">
+      <install version="1.0">
+            <actions>
+              <action type="download_by_url">https://pypi.python.org/packages/source/M/MACS2/MACS2-2.1.0.20140616.tar.gz</action>
+	      <!-- Install environment for main & test toolsheds -->
+              <action type="set_environment_for_install">
+		<repository changeset_revision="84e97f5cd3ab" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+		  <package name="numpy" version="1.9" />
+		</repository>
+	      </action>
+              <action type="make_directory">$INSTALL_DIR/lib/python</action>
+              <action type="shell_command">
+                export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
+                python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
+              </action>
+              <action type="set_environment">
+                <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+              </action>
+            </actions>
+      </install>
+      <readme>Macs2.1 depends on having python2.7 and numpy 1.8 installed on all nodes of the work cluster</readme>
+    </package>
+</tool_dependency>