# HG changeset patch
# User yhoogstrate
# Date 1433332609 14400
# Node ID 88696b8f774b93c78d797da86c00a8a06bef2c87

planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/package_flaimapper_1_2_1 commit 18c2fff1b59feb43640d744444d8fb6193def183-dirty

diff -r 000000000000 -r 88696b8f774b tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Jun 03 07:56:49 2015 -0400
@@ -0,0 +1,60 @@
+<?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>
+</tool_dependency>