# HG changeset patch
# User Matt Shirley <mdshw5@gmail.com>
# Date 1427746947 14400
# Node ID dd337a830b5cb55a9fcbfabccc7a055b2808ce33
# Parent  c71031b17e083d819cbaccdbcd320e676baea47e
Use patched versions of tools.

diff -r c71031b17e08 -r dd337a830b5c tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Mar 30 15:05:20 2015 -0400
+++ b/tool_dependencies.xml	Mon Mar 30 16:22:27 2015 -0400
@@ -6,19 +6,16 @@
         <action type="make_directory">src</action>
         <action type="make_directory">build</action>
         <action type="change_directory">src</action>
-        <action type="shell_command">git clone https://github.com/ncbi/sra-tools.git</action>
-        <action type="shell_command">git clone https://github.com/ncbi/ncbi-vdb.git</action>
-        <action type="shell_command">git clone https://github.com/ncbi/ngs.git</action>
+        <action type="shell_command">git clone https://github.com/mdshw5/sra-tools.git</action>
+        <action type="shell_command">git clone https://github.com/mdshw5/ncbi-vdb.git</action>
+        <action type="shell_command">git clone https://github.com/mdshw5/ngs.git</action>
         <action type="shell_command">LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib</action>
         <action type="change_directory">ncbi-vdb</action>
-        <action type="shell_command">git checkout bf5ffdd</action>
         <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action>
         <action type="change_directory">../ngs</action>
-        <action type="shell_command">git checkout 3a7a0ed</action>
         <action type="change_directory">ngs-sdk</action>
         <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action>
         <action type="change_directory">../../sra-tools</action>
-        <action type="shell_command">git checkout 4ef7ea0</action>
         <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build --with-ncbi-vdb-build=$INSTALL_DIR/build --with-ncbi-vdb-sources=$INSTALL_DIR/src/ncbi-vdb --with-ngs-sdk-prefix=$INSTALL_DIR --with-magic-prefix=/dev/null</action>
         <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/ncbi/default.kfg</action>
       </actions>