# HG changeset patch
# User Matt Shirley <mdshw5@gmail.com>
# Date 1427740845 14400
# Node ID 3369a52a5934989ebe86639bc01b4e52b861b362
# Parent  d45b5bdcff3fd0cec1413fc621967f10bc0b1d11
Set environment variables using shell.

diff -r d45b5bdcff3f -r 3369a52a5934 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Mar 30 14:27:49 2015 -0400
+++ b/tool_dependencies.xml	Mon Mar 30 14:40:45 2015 -0400
@@ -2,29 +2,24 @@
 <tool_dependency>
   <package name="sra_toolkit" version="2.4.5">
     <install version="1.0">
-      <actions>
-        <action type="set_environment">
-          <environment_variable name="NCBI" action="set_to">$PWD/ncbi</environment_variable>
-          <environment_variable name="BUILD" action="set_to">$PWD/build</environment_variable>
-          <environment_variable name="LD_LIBRARY_PATH" action="append_to">$INSTALL_DIR/lib64</environment_variable>
-          <environment_variable name="LD_LIBRARY_PATH" action="append_to">$INSTALL_DIR/lib</environment_variable>
-        </action>
-        <action type="make_directory">$BUILD</action>
-        <action type="make_directory">$NCBI</action>
-        <action type="change_directory">$NCBI</action>
+
+        <action type="make_directory">ncbi</action>
+        <action type="make_directory">ncbi/build</action>
+        <action type="change_directory">ncbi</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">cd $NCBI/ncbi-vdb</action>
+        <action type="shell_command">LD_LIBRARY_PATH=LD_LIBRARY_PATH:$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=$BUILD</action>
-        <action type="shell_command">cd $NCBI/ngs</action>
+        <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=../build</action>
+        <action type="change_directory">../ngs</action>
         <action type="shell_command">git checkout 3a7a0ed</action>
-        <action type="shell_command">cd $NCBI/ngs/ngs-sdk</action>
-        <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$BUILD</action>
-        <action type="shell_command">cd $NCBI/sra-tools</action>
+        <action type="change_directory">ngs-sdk</action>
+        <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=../../build</action>
+        <action type="change_directory">../../sra-tools</action>
         <action type="shell_command">git checkout 4ef7ea0</action>
-        <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$BUILD --with-ncbi-vdb-build=$BUILD --with-ncbi-vdb-sources=$NCBI/ncbi-vdb --with-ngs-sdk-prefix=$INSTALL_DIR --with-magic-prefix=/dev/null</action>
+        <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=../build --with-ncbi-vdb-build=../build --with-ncbi-vdb-sources=../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>
     </install>