Mercurial > repos > matt-shirley > ncbi_sra_toolkit

comparison tool_dependencies.xml @ 17:a8261e9cbe13

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Add install directory to PATH.
author Matt Shirley <mdshw5@gmail.com>
date Mon, 30 Mar 2015 20:24:04 -0400
parents dd337a830b5c
children 3da3d1a4deae
comparison
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16:dd337a830b5c 17:a8261e9cbe13
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.