Mercurial > repos > matt-shirley > ncbi_sra_toolkit
diff tool_dependencies.xml @ 12:d45b5bdcff3f
Don't use builtin change_directory directive
| author | Matt Shirley <mdshw5@gmail.com> |
|---|---|
| date | Mon, 30 Mar 2015 14:27:49 -0400 |
| parents | 91558de676f4 |
| children | 3369a52a5934 |
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--- a/tool_dependencies.xml Mon Mar 30 14:06:16 2015 -0400 +++ b/tool_dependencies.xml Mon Mar 30 14:27:49 2015 -0400 @@ -15,14 +15,14 @@ <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="change_directory">$NCBI/ncbi-vdb</action> + <action type="shell_command">cd $NCBI/ncbi-vdb</action> <action type="shell_command">git checkout bf5ffdd</action> <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$BUILD</action> - <action type="change_directory">$NCBI/ngs</action> + <action type="shell_command">cd $NCBI/ngs</action> <action type="shell_command">git checkout 3a7a0ed</action> - <action type="change_directory">$NCBI/ngs/ngs-sdk</action> + <action type="shell_command">cd $NCBI/ngs/ngs-sdk</action> <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$BUILD</action> - <action type="change_directory">$NCBI/sra-tools</action> + <action type="shell_command">cd $NCBI/sra-tools</action> <action type="shell_command">git checkout 4ef7ea0</action> <action type="autoconf">--prefix=$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="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/ncbi/default.kfg</action>