diff tool_dependencies.xml @ 0:f411ce97a351 draft

Uploaded initial version 1.0.2-2

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,114 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <!-- Local version of R 3.1.2 dependency -->
+  <package name="R" version="3.1.2">
+    <install version="1.0">
+      <actions>
+	<action type="download_by_url">http://cran.r-project.org/src/base/R-3/R-3.1.2.tar.gz</action>
+        <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
+        <action type="make_install" />
+        <action type="set_environment">
+          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+        </action>
+      </actions>
+    </install>
+  </package>
+  <!-- Python mysqldb package -->
+  <package name="python_mysqldb" version="1.2.5">
+    <install version="1.0">
+      <actions>
+	<action type="download_by_url">https://pypi.python.org/packages/source/M/MySQL-python/MySQL-python-1.2.5.zip</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">$INSTALL_DIR/bin</environment_variable>
+        </action>
+      </actions>
+    </install>
+    <readme>Installs Python module MySQLdb 1.2.5</readme>
+  </package>
+  <!-- bx_python
+       This is cribbed from devteam's 'package_bx_python_0_7' in the main
+       toolshed:
+       https://toolshed.g2.bx.psu.edu/view/devteam/package_bx_python_0_7
+  -->
+  <package name="bx_python" version="0.7.1">
+    <install version="1.0">
+      <actions>
+        <action type="setup_virtualenv">
+numpy==1.7.1
+bx-python==0.7.1
+        </action>
+        <action type="set_environment">
+          <environment_variable action="set_to" name="BX_PYTHON_PATH">$INSTALL_DIR</environment_variable>
+        </action>
+      </actions>
+    </install>
+    <readme>
+      Installation of bx-python 0.7.1 along with numpy 1.7.1. The installation can be
+      accessed via BX_PYTHON_PATH.
+    </readme>
+  </package>
+  <!-- cistrome_ceas
+       Installs the version of CEAS package found in the Cistrome
+       distribution:
+       https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
+  -->
+  <package name="cistrome_ceas" version="1.0.2.d8c0751">
+    <install version="1.0">
+      <actions>
+	<action type="shell_command">
+	  hg clone https://bitbucket.org/cistrome/cistrome-applications-harvard cistrome_ceas
+	</action>
+	<action type="shell_command">
+	  hg update d8c0751
+	</action>
+        <action type="make_directory">$INSTALL_DIR/lib/python</action>
+        <action type="shell_command">
+	  cd published-packages/CEAS/
+          export PYTHONPATH=$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">$INSTALL_DIR/bin</environment_variable>
+        </action>
+      </actions>
+    </install>
+    <readme>Installs version 1.0.2 of CEAS from cistrome (commit id d8c0751,
+    datestamp 20140929), which includes ceasBW (a version of ceas which can
+    handle bigWig file input from MACS2.
+
+    Cistrome code is at
+    https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
+      
+    The CEAS code is under the published-packages/CEAS/ subdirectory
+
+    Cistrome data files and documentation can be found at
+    http://liulab.dfci.harvard.edu/CEAS/index.html
+    </readme>
+  </package>
+  <!-- fetchChromSize from UCSC tools -->
+  <package name="ucsc_fetchChromSizes" version="1.0">
+      <install version="1.0">
+        <actions>
+          <action type="download_binary">
+            <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes</url_template>
+          </action>
+          <action type="chmod">
+            <file mode="755">$INSTALL_DIR/fetchChromSizes</file>
+          </action>
+          <action type="set_environment">
+            <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
+        </action>
+	</actions>
+      </install>
+    <readme>Installs the binary executable for the fetchChromSizes utility
+    from UCSC tools
+    </readme>
+  </package>
+</tool_dependency>