# HG changeset patch
# User yhoogstrate
# Date 1438333628 14400
# Node ID 6262f77f889a8682abb25a2d337a86a4806b36ea
# Parent  88696b8f774b93c78d797da86c00a8a06bef2c87
Uploaded

diff -r 88696b8f774b -r 6262f77f889a tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jun 03 07:56:49 2015 -0400
+++ b/tool_dependencies.xml	Fri Jul 31 05:07:08 2015 -0400
@@ -1,60 +1,65 @@
 <?xml version="1.0"?>
 <tool_dependency>
-	<!--
-		pysam has had several internal changes in 0.7.*, 0.8.1, 0.8.2 &
-		0.8.3 and therefore FlaiMapper is not compatible with all of
-		them. For compatibility this package is provided with pysam
-		0.8.2.1 which was not originally in the toolshed.
-	-->
-	<package name="pysam" version="0.8.2.1">
-		<repository changeset_revision="b8d22acd3017" name="package_pysam_0_8_2" owner="yhoogstrate" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-	</package>
-	
-	<package name="flaimapper" version="1.2.1">
-		<install version="1.0">
-			<actions>
-				<action type="set_environment_for_install">
-					<repository changeset_revision="b8d22acd3017" name="package_pysam_0_8_2" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu">
-						<package name="pysam" version="0.8.2.1" />
-					</repository>
-				</action>
-				
-				<action type="make_directory">$INSTALL_DIR/bin</action>
-				<action type="make_directory">$INSTALL_DIR/lib/python</action>
-				<action type="make_directory">$INSTALL_DIR/lib64/python</action>
-				
-				<action type="shell_command">
-					git clone https://github.com/yhoogstrate/flaimapper flaimapper	&amp;&amp;
-					cd flaimapper													&amp;&amp;
-					git reset --hard d3cc32a10ba3d33fde4cb76e8013a51ec8bdf779		&amp;&amp;
-					
-					export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR						&amp;&amp;
-					export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR"/lib/python"			&amp;&amp;
-					export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR"/lib64/python"		&amp;&amp;
-					export PYTHONPATH=$PYTHONPATH:$PYSAM_PATH						&amp;&amp;
-					export PYTHONPATH=$PYTHONPATH:$PYSAM_PATH"/lib/python"			&amp;&amp;
-					export PYTHONPATH=$PYTHONPATH:$PYSAM_PATH"/lib64/python"		&amp;&amp;
-					
-					cd src															&amp;&amp;
-					
-					python setup.py build											&amp;&amp;
-					python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin
-				</action>
-				
-				<action type="set_environment">
-					<environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
-					<environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-				</action>
-			</actions>
-		</install>
-		
-		<readme>
-			Downloads and installs FlaiMapper. Prerequisites:
-				- git
-			
-			Because I accidentally included too much large files within
-			the GitHub repository of FlaiMapper it has become large.
-			This explains why installation takes a while.
-		</readme>
-	</package>
+    <!--
+        pysam has had several internal changes in 0.7.*, 0.8.1, 0.8.2 &
+        0.8.3 and therefore FlaiMapper is not compatible with all of
+        them. For compatibility this package is provided with pysam
+        0.8.2.1 which was not originally in the toolshed.
+    -->
+    <package name="pysam" version="0.8.2.1">
+        <repository changeset_revision="b8d22acd3017" name="package_pysam_0_8_2" owner="yhoogstrate" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    
+    <package name="flaimapper" version="1.2.1">
+        <install version="1.0">
+            <actions>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="b8d22acd3017" name="package_pysam_0_8_2" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="pysam" version="0.8.2.1" />
+                    </repository>
+                </action>
+                
+                <action type="make_directory">$INSTALL_DIR/bin</action>
+                <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                <action type="make_directory">$INSTALL_DIR/lib64/python</action>
+                
+                <action type="shell_command">
+                    git clone https://github.com/yhoogstrate/flaimapper flaimapper &amp;&amp;
+                    cd flaimapper                                                  &amp;&amp;
+                    git reset --hard d3cc32a10ba3d33fde4cb76e8013a51ec8bdf779      &amp;&amp;
+                    
+                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR                     &amp;&amp;
+                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR"/lib/python"        &amp;&amp;
+                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR"/lib64/python"      &amp;&amp;
+                    export PYTHONPATH=$PYTHONPATH:$PYSAM_PATH                      &amp;&amp;
+                    export PYTHONPATH=$PYTHONPATH:$PYSAM_PATH"/lib/python"         &amp;&amp;
+                    export PYTHONPATH=$PYTHONPATH:$PYSAM_PATH"/lib64/python"       &amp;&amp;
+                    
+                    cd src                                                         &amp;&amp;
+                    
+                    python setup.py build                                          &amp;&amp;
+                    python setup.py install
+                        --home $INSTALL_DIR
+                        --install-scripts $INSTALL_DIR/bin
+                </action>
+                
+                <action type="set_environment">
+                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        
+        <readme>
+            Downloads and installs FlaiMapper.
+            
+            Prerequisites:
+                - Python
+                - git
+            
+            Because I accidentally included too much large files within
+            the GitHub repository of FlaiMapper, it has become large.
+            This is the reason why installation takes a while.
+        </readme>
+    </package>
 </tool_dependency>