Mercurial > repos > matt-shirley > ncbi_sra_toolkit

diff tool_dependencies.xml @ 15:c71031b17e08

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Avoid relative paths, and rename "ncbi" dir
author Matt Shirley <mdshw5@gmail.com>
date Mon, 30 Mar 2015 15:05:20 -0400
parents ef71f5982df5
children dd337a830b5c
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--- a/tool_dependencies.xml	Mon Mar 30 14:43:05 2015 -0400
+++ b/tool_dependencies.xml	Mon Mar 30 15:05:20 2015 -0400
@@ -3,23 +3,23 @@
   <package name="sra_toolkit" version="2.4.5">
     <install version="1.0">
       <actions>
-        <action type="make_directory">ncbi</action>
-        <action type="make_directory">ncbi/build</action>
-        <action type="change_directory">ncbi</action>
+        <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">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=$INSTALL_DIR --build-prefix=../build</action>
+        <action type="autoconf">--prefix=$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=../../build</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=$INSTALL_DIR --build-prefix=../build --with-ncbi-vdb-build=../build --with-ncbi-vdb-sources=../ncbi-vdb --with-ngs-sdk-prefix=$INSTALL_DIR --with-magic-prefix=/dev/null</action>
+        <action type="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>
     </install>