# HG changeset patch
# User jeremie
# Date 1404209733 14400
# Node ID 45d4731e884fafb97d23805bfc96603f14e41399
# Parent  66b145be8b33ed67d6a84fd2bedb61ce4e043da4
Uploaded

diff -r 66b145be8b33 -r 45d4731e884f tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jul 01 06:03:22 2014 -0400
+++ b/tool_dependencies.xml	Tue Jul 01 06:15:33 2014 -0400
@@ -21,22 +21,32 @@
                         <source>bin/breakdancer-max</source>
                         <destination>$INSTALL_DIR/bin</destination>
                     </action>
-                    <action type="download_by_url">http://vt58zikphf.1fichier.com/bam2cfg.pl</action>
                     <action type="move_file">
-                        <source>bam2cfg.pl</source>
+                        <source>../perl/bam2cfg.pl</source>
                         <destination>$INSTALL_DIR/bin</destination>
                     </action>
-                    <!-- http://9ypffrj86h.1fichier.com/ -->
-                    <!--  <action type="download_by_url">http://7cv3od97gg.1fichier.com/1_2_6.tar.gz</action>
-                    -->    
-                    <action type="shell_command">ls</action>
+                    <!-- <action type="download_by_url">http://9ypffrj86h.1fichier.com/breakdancer2vcf.py</action> -->
+                    <action type="shell_command">git clone https://github.com/ALLBio/allbiotc2/blob/master/breakdancer/breakdancer2vcf.py</action>
+                    <!-- <action type="shell_command">ls</action>
                     <action type="shell_command">pwd</action>
                     <action type="change_directory">..</action>
                     <action type="shell_command">ls</action>
                     <action type="shell_command">pwd</action>
                     <action type="change_directory">..</action>
                     <action type="shell_command">ls</action>
+                    <action type="shell_command">pwd</action> -->
+                    <action type="move_file">
+                        <source>breakdancer2vcf.py</source>
+                        <destination>$INSTALL_DIR/bin</destination>
+                    </action>
+                    <!-- <action type="shell_command">ls</action>
                     <action type="shell_command">pwd</action>
+                    <action type="change_directory">..</action>
+                    <action type="shell_command">ls</action>
+                    <action type="shell_command">pwd</action>
+                    <action type="change_directory">..</action>
+                    <action type="shell_command">ls</action>
+                    <action type="shell_command">pwd</action> -->
                     <!-- <action type="move_directory_files">
                         <source_directory>../../1_2_6</source_directory>
                         <destination_directory>$INSTALL_DIR/bin</destination_directory>