# HG changeset patch
# User Matt Shirley <mdshw5@gmail.com>
# Date 1427762658 14400
# Node ID 6d25dfb4dbb404e16fb3994d166e42f26dbaede1
# Parent  3da3d1a4deaef2375e5b3fe042ca23ba355c6381
Trying this again.

diff -r 3da3d1a4deae -r 6d25dfb4dbb4 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Mar 30 20:31:50 2015 -0400
+++ b/tool_dependencies.xml	Mon Mar 30 20:44:18 2015 -0400
@@ -6,15 +6,17 @@
         <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/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="shell_command">cd $INSTALL_DIR/src/ncbi-vdb</action>
+        <action type="shell_command">
+            git clone https://github.com/mdshw5/sra-tools.git
+            git clone https://github.com/mdshw5/ncbi-vdb.git
+            git clone https://github.com/mdshw5/ngs.git
+            LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib
+        </action>
+        <action type="change_directory">./ncbi-vdb</action>
         <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action>
-        <action type="shell_command">cd $INSTALL_DIR/src/ngs/ngs-sdk</action>
+        <action type="change_directory">../ngs/ngs-sdk</action>
         <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action>
-        <action type="shell_command"> cd $INSTALL_DIR/src/sra-tools</action>
+        <action type="change_directory">../../sra-tools</action>
         <action type="autoconf">--prefix=$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\"|" $INSTALL_DIR/ncbi/default.kfg</action>
         <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action>