# HG changeset patch
# User yhoogstrate
# Date 1426864472 14400
# Node ID ab3ea877607f8bc815f6ebe69a8451c371599fdc
# Parent  0e9520cf7587c594d514d4c287455761880ebbb0
Uploaded

diff -r 0e9520cf7587 -r ab3ea877607f README.rst
--- a/README.rst	Fri Mar 20 10:45:21 2015 -0400
+++ b/README.rst	Fri Mar 20 11:14:32 2015 -0400
@@ -29,7 +29,7 @@
 
 **pysam**:
 
-The MIT License (>=3)
+The MIT License
 
 References
 ----------
diff -r 0e9520cf7587 -r ab3ea877607f egg/flaimapper-1.1.4-py2.7.egg
Binary file egg/flaimapper-1.1.4-py2.7.egg has changed
diff -r 0e9520cf7587 -r ab3ea877607f egg/flaimapper-1.1.5-py2.7.egg
Binary file egg/flaimapper-1.1.5-py2.7.egg has changed
diff -r 0e9520cf7587 -r ab3ea877607f flaimapper.xml
--- a/flaimapper.xml	Fri Mar 20 10:45:21 2015 -0400
+++ b/flaimapper.xml	Fri Mar 20 11:14:32 2015 -0400
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="flaimapper" name="FlaiMapper" version="1.1.4.a">
+<tool id="flaimapper" name="FlaiMapper" version="1.1.5.a">
 	<description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description>
 	<requirements>
-		<requirement type="package" version="0.8.2.1">pysam</requirement><!-- pysam 0.7.7 ABSOLUTELY CRASHES !!! -->
-		<requirement type="package" version="1.1.4">flaimapper</requirement>
+		<requirement type="package" version="0.8.2.1">pysam</requirement>
+		<requirement type="package" version="1.1.5">flaimapper</requirement>
 	</requirements>
 	
 	<version_command>flaimapper --version</version_command>
@@ -62,6 +62,21 @@
 
 The reference sequence should be provided in FASTSA format.
 
+You can access **ncRNAdb09** at the following URLs:
+https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.gtf *(mask file)*
+https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)*
+
+Therefore you need bam files aligned to the same reference. We have made
+the following available:
+
+ - **Tophat1**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz
+ - **Tophat2**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz
+
+If you want to test flaimapper with example data you can obtain several
+alignment files from this following directory tree:
+
+https://github.com/yhoogstrate/flaimapper/tree/master/share/small_RNA-seq_alignments
+
 Installation
 ------------
 
@@ -77,7 +92,7 @@
 
 **pysam**:
 
-The MIT License (>=3)
+The MIT License
 
 Contact
 -------
diff -r 0e9520cf7587 -r ab3ea877607f tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Mar 20 10:45:21 2015 -0400
+++ b/tool_dependencies.xml	Fri Mar 20 11:14:32 2015 -0400
@@ -4,7 +4,7 @@
 		<repository changeset_revision="e6c1f548397a" name="package_pysam_0_8_2" owner="yhoogstrate" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 	</package>
 	
-	<package name="flaimapper" version="1.1.4">
+	<package name="flaimapper" version="1.1.5">
 		<install version="1.0">
 			<actions>
 				
@@ -17,7 +17,7 @@
 				<action type="make_directory">$INSTALL_DIR</action>
 				<action type="make_directory">$INSTALL_DIR/bin</action>
 				
-				<action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR:$INSTALL_DIR"/lib/python":$INSTALL_DIR"/lib64/python":$PYSAM_PATH:$PYSAM_PATH"/lib/python":$PYSAM_PATH"/lib64/python" ; easy_install --prefix=$INSTALL_DIR --install-dir=$INSTALL_DIR --script-dir=$INSTALL_DIR/bin $REPOSITORY_INSTALL_DIR"/egg/flaimapper-1.1.4-py2.7.egg"</action>
+				<action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR:$INSTALL_DIR"/lib/python":$INSTALL_DIR"/lib64/python":$PYSAM_PATH:$PYSAM_PATH"/lib/python":$PYSAM_PATH"/lib64/python" ; easy_install --prefix=$INSTALL_DIR --install-dir=$INSTALL_DIR --script-dir=$INSTALL_DIR/bin $REPOSITORY_INSTALL_DIR"/egg/flaimapper-1.1.5-py2.7.egg"</action>
 				
 				<action type="set_environment">
 					<environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>