# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1406304798 18000
# Node ID 9dc3a38a440eecd3d1f07dc6bd553738b55b3971
# Parent  53ed3caf1d9df626b4c67c9f26e1a0ec9fd17381
Add extract_splice_sites.py for converting GTF files

diff -r 53ed3caf1d9d -r 9dc3a38a440e tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jul 22 08:45:16 2014 -0400
+++ b/tool_dependencies.xml	Fri Jul 25 11:13:18 2014 -0500
@@ -21,6 +21,10 @@
                         <source>hisat-inspect</source>
                         <destination>$INSTALL_DIR/bin</destination>
                     </action>
+                    <action type="move_file">
+                        <source>extract_splice_sites.py</source>
+                        <destination>$INSTALL_DIR/bin</destination>
+                    </action>
                 </actions>
                 <actions architecture="x86_64" os="darwin">
                     <action type="download_by_url">http://ccb.jhu.edu/software/hisat/downloads/hisat-0.1.0-beta-OSX_x86_64.zip</action>
@@ -40,6 +44,10 @@
                         <source>hisat-inspect</source>
                         <destination>$INSTALL_DIR/bin</destination>
                     </action>
+                    <action type="move_file">
+                        <source>extract_splice_sites.py</source>
+                        <destination>$INSTALL_DIR/bin</destination>
+                    </action>
                 </actions>
                 <actions>
                     <action type="download_by_url">http://ccb.jhu.edu/software/hisat/downloads/hisat-0.1.0-beta-source.zip</action>
@@ -60,6 +68,10 @@
                         <source>hisat-inspect</source>
                         <destination>$INSTALL_DIR/bin</destination>
                     </action>
+                    <action type="move_file">
+                        <source>extract_splice_sites.py</source>
+                        <destination>$INSTALL_DIR/bin</destination>
+                    </action>
                 </actions>
             </actions_group>
             <actions>
@@ -75,6 +87,9 @@
                 <action type="chmod">
                     <file mode="750">$INSTALL_DIR/bin/hisat-inspect</file>
                 </action>
+                <action type="chmod">
+                    <file mode="750">$INSTALL_DIR/bin/extract_splice_sites.py</file>
+                </action>
                 <action type="set_environment">
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                 </action>