diff tool_dependencies.xml @ 2:b6ccc7dd7b02 draft

Version 0.02.04.3.

--- a/tool_dependencies.xml	Mon Mar 23 07:01:37 2015 -0400
+++ b/tool_dependencies.xml	Fri Dec 04 07:43:30 2015 -0500
@@ -64,4 +64,39 @@
       </install>
       <readme>primer3_core</readme>
     </package>
+    <package name="biopython" version="1.65">
+      <install version="1.0">
+	<actions>
+	  <action type="shell_command">pip install  --install-option "--prefix=$INSTALL_DIR" https://pypi.python.org/packages/source/b/biopython/biopython-1.65.tar.gz</action>
+	  <action type="set_environment">
+	    <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib/python2.7/site-packages</environment_variable>
+	    <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib64/python2.7/site-packages</environment_variable>
+	  </action>
+	</actions>
+      </install>
+      <readme>BioPython 1.65</readme>
+    </package>
+    <package name="pandaseq" version="2.8.1">
+      <install version="1.0">
+	<actions>
+	  <action type="download_by_url">https://github.com/neufeld/pandaseq/archive/v2.8.1.tar.gz</action>
+	  <action type="shell_command">./autogen.sh</action>
+	  <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
+	  <action type="shell_command">make</action>
+	  <action type="shell_command">make install</action>
+	  <action type="set_environment">
+	    <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>
+	  </action>
+	</actions>
+      </install>
+      <readme>PANDASeq 2.8.1
+
+      PANDASEQ is a program to align Illumina reads, optionally
+      with PCR primers embedded in the sequence, and reconstruct
+      an overlapping sequence.
+
+      https://github.com/neufeld/pandaseq
+      </readme>
+    </package>
 </tool_dependency>