# HG changeset patch
# User yhoogstrate
# Date 1426779656 14400
# Node ID 5e677aafc3a1a9a69b9f4abc1441b2b6f593bed5
# Parent  ed32b1282a170bbed45b0ddde34f5427bb9b4060
Uploaded

diff -r ed32b1282a17 -r 5e677aafc3a1 README.md
diff -r ed32b1282a17 -r 5e677aafc3a1 README.rst
diff -r ed32b1282a17 -r 5e677aafc3a1 flaimapper.xml
--- a/flaimapper.xml	Thu Mar 19 10:51:14 2015 -0400
+++ b/flaimapper.xml	Thu Mar 19 11:40:56 2015 -0400
@@ -2,10 +2,7 @@
 <tool id="flaimapper" name="FlaiMapper" version="1.1.2.a">
 	<description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description>
 	<requirements>
-		<requirement type="package" version="0.7.7">pysam</requirement>
-		<!--
-		<requirement type="package" version="0.8.1">pysam</requirement>
-		-->
+		<requirement type="package" version="0.8.1">pysam</requirement><!-- pysam 0.7.7 ABSOLUTELY CRASHES !!! -->
 		<requirement type="package" version="1.1.2">flaimapper</requirement>
 	</requirements>
 	
diff -r ed32b1282a17 -r 5e677aafc3a1 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Mar 19 10:51:14 2015 -0400
+++ b/tool_dependencies.xml	Thu Mar 19 11:40:56 2015 -0400
@@ -1,29 +1,27 @@
 <?xml version="1.0"?>
 <tool_dependency>
-	<package name="pysam" version="0.7.7">
-		<repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-	</package>
+	<!--
+		Because I accidentally included too much large files within the
+		GitHub repository of FlaiMapper it is not convenient to use git
+		to pull the latest code from. Downloading simply takes way to
+		long and the package size is unnecessairy large.
+		
+		Instead, I have created an egg that can be installed using
+		easy_install.
+	-->
 	
-	<!--
 	<package name="pysam" version="0.8.1">
-		<repository name="package_pysam_0_8_1" owner="iuc" prior_installation_required="True" />
+		<repository changeset_revision="6b6843e15541" name="package_pysam_0_8_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 	</package>
-	-->
 	
 	<package name="flaimapper" version="1.1.2">
 		<install version="1.0">
 			<actions>
 				
 				<action type="set_environment_for_install">
-					<repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-						<package name="pysam" version="0.7.7" />
-					</repository>
-					
-					<!--
-					<repository name="package_pysam_0_8_1" owner="iuc">
+					<repository changeset_revision="6b6843e15541" name="package_pysam_0_8_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
 						<package name="pysam" version="0.8.1" />
 					</repository>
-					-->
 				</action>
 				
 				<action type="make_directory">$INSTALL_DIR</action>