# HG changeset patch
# User Matt Shirley <mdshw5@gmail.com>
# Date 1427764263 14400
# Node ID 847db227d9ce1938c154e0f0935e3be77b06df4a
# Parent  281f34ece271f46082c3cd22ef2ed61ef4786a19
OK now.

diff -r 281f34ece271 -r 847db227d9ce tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Mar 30 20:59:06 2015 -0400
+++ b/tool_dependencies.xml	Mon Mar 30 21:11:03 2015 -0400
@@ -11,15 +11,20 @@
             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
+            cd $INSTALL_DIR/ncbi-vdb
+            ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
+            make -j2
+            make install
+            cd $INSTALL_DIR/ngs/ngs-sdk
+            ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
+            make -j2
+            make install
+            cd $INSTALL_DIR/sra-tools
+            ./configure --prefix=$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
+            make -j2
+            make install
+            sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/lib64/ncbi/default.kfg
         </action>
-        <action type="change_directory">./ncbi-vdb</action>
-        <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action>
-        <action type="change_directory">../ngs/ngs-sdk</action>
-        <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action>
-        <action type="change_directory">../../sra-tools</action>
-        <action type="shell_command">echo $PWD</action>
-        <action type="autoconf">--prefix=$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>
       </actions>
     </install>