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comparison tool_dependencies.xml @ 13:3369a52a5934

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Set environment variables using shell.
author Matt Shirley <mdshw5@gmail.com>
date Mon, 30 Mar 2015 14:40:45 -0400
parents d45b5bdcff3f
children ef71f5982df5
comparison
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12:d45b5bdcff3f 13:3369a52a5934
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="sra_toolkit" version="2.4.5"> 3 <package name="sra_toolkit" version="2.4.5">
4 <install version="1.0"> 4 <install version="1.0">
5 <actions> 5
6 <action type="set_environment"> 6 <action type="make_directory">ncbi</action>
7 <environment_variable name="NCBI" action="set_to">$PWD/ncbi</environment_variable> 7 <action type="make_directory">ncbi/build</action>
8 <environment_variable name="BUILD" action="set_to">$PWD/build</environment_variable> 8 <action type="change_directory">ncbi</action>
9 <environment_variable name="LD_LIBRARY_PATH" action="append_to">$INSTALL_DIR/lib64</environment_variable>
10 <environment_variable name="LD_LIBRARY_PATH" action="append_to">$INSTALL_DIR/lib</environment_variable>
11 </action>
12 <action type="make_directory">$BUILD</action>
13 <action type="make_directory">$NCBI</action>
14 <action type="change_directory">$NCBI</action>
15 <action type="shell_command">git clone https://github.com/ncbi/sra-tools.git</action> 9 <action type="shell_command">git clone https://github.com/ncbi/sra-tools.git</action>
16 <action type="shell_command">git clone https://github.com/ncbi/ncbi-vdb.git</action> 10 <action type="shell_command">git clone https://github.com/ncbi/ncbi-vdb.git</action>
17 <action type="shell_command">git clone https://github.com/ncbi/ngs.git</action> 11 <action type="shell_command">git clone https://github.com/ncbi/ngs.git</action>
18 <action type="shell_command">cd $NCBI/ncbi-vdb</action> 12 <action type="shell_command">LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib</action>
13 <action type="change_directory">ncbi-vdb</action>
19 <action type="shell_command">git checkout bf5ffdd</action> 14 <action type="shell_command">git checkout bf5ffdd</action>
20 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$BUILD</action> 15 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=../build</action>
21 <action type="shell_command">cd $NCBI/ngs</action> 16 <action type="change_directory">../ngs</action>
22 <action type="shell_command">git checkout 3a7a0ed</action> 17 <action type="shell_command">git checkout 3a7a0ed</action>
23 <action type="shell_command">cd $NCBI/ngs/ngs-sdk</action> 18 <action type="change_directory">ngs-sdk</action>
24 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$BUILD</action> 19 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=../../build</action>
25 <action type="shell_command">cd $NCBI/sra-tools</action> 20 <action type="change_directory">../../sra-tools</action>
26 <action type="shell_command">git checkout 4ef7ea0</action> 21 <action type="shell_command">git checkout 4ef7ea0</action>
27 <action type="autoconf">--prefix=$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> 22 <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>
28 <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/ncbi/default.kfg</action> 23 <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/ncbi/default.kfg</action>
29 </actions> 24 </actions>
30 </install> 25 </install>
31 <readme> 26 <readme>
32 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives. 27 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.