Mercurial > repos > matt-shirley > ncbi_sra_toolkit
comparison tool_dependencies.xml @ 17:a8261e9cbe13
Add install directory to PATH.
author | Matt Shirley <mdshw5@gmail.com> |
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date | Mon, 30 Mar 2015 20:24:04 -0400 |
parents | dd337a830b5c |
children | 3da3d1a4deae |
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16:dd337a830b5c | 17:a8261e9cbe13 |
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8 <action type="change_directory">src</action> | 8 <action type="change_directory">src</action> |
9 <action type="shell_command">git clone https://github.com/mdshw5/sra-tools.git</action> | 9 <action type="shell_command">git clone https://github.com/mdshw5/sra-tools.git</action> |
10 <action type="shell_command">git clone https://github.com/mdshw5/ncbi-vdb.git</action> | 10 <action type="shell_command">git clone https://github.com/mdshw5/ncbi-vdb.git</action> |
11 <action type="shell_command">git clone https://github.com/mdshw5/ngs.git</action> | 11 <action type="shell_command">git clone https://github.com/mdshw5/ngs.git</action> |
12 <action type="shell_command">LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib</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> | 13 <action type="change_directory">$INSTALL_DIR/src/ncbi-vdb</action> |
14 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action> | 14 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action> |
15 <action type="change_directory">../ngs</action> | 15 <action type="change_directory">$INSTALL_DIR/src/ngs/ngs-sdk</action> |
16 <action type="change_directory">ngs-sdk</action> | |
17 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action> | 16 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action> |
18 <action type="change_directory">../../sra-tools</action> | 17 <action type="change_directory">$INSTALL_DIR/src/sra-tools</action> |
19 <action type="autoconf">--prefix=$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> | 18 <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=$INSTALL_DIR --with-magic-prefix=/dev/null</action> |
20 <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/ncbi/default.kfg</action> | 19 <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/ncbi/default.kfg</action> |
20 <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> | |
21 </actions> | 21 </actions> |
22 </install> | 22 </install> |
23 <readme> | 23 <readme> |
24 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives. | 24 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives. |
25 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures. | 25 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures. |