Mercurial > repos > matt-shirley > ncbi_sra_toolkit

comparison 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
comparison
equal deleted inserted replaced
14:ef71f5982df5 15:c71031b17e08
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 <actions>
6 <action type="make_directory">ncbi</action> 6 <action type="make_directory">src</action>
7 <action type="make_directory">ncbi/build</action> 7 <action type="make_directory">build</action>
8 <action type="change_directory">ncbi</action> 8 <action type="change_directory">src</action>
9 <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>
10 <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>
11 <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>
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">ncbi-vdb</action>
14 <action type="shell_command">git checkout bf5ffdd</action> 14 <action type="shell_command">git checkout bf5ffdd</action>
15 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=../build</action> 15 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action>
16 <action type="change_directory">../ngs</action> 16 <action type="change_directory">../ngs</action>
17 <action type="shell_command">git checkout 3a7a0ed</action> 17 <action type="shell_command">git checkout 3a7a0ed</action>
18 <action type="change_directory">ngs-sdk</action> 18 <action type="change_directory">ngs-sdk</action>
19 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=../../build</action> 19 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action>
20 <action type="change_directory">../../sra-tools</action> 20 <action type="change_directory">../../sra-tools</action>
21 <action type="shell_command">git checkout 4ef7ea0</action> 21 <action type="shell_command">git checkout 4ef7ea0</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> 22 <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=$INSTALL_DIR --with-magic-prefix=/dev/null</action>
23 <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/ncbi/default.kfg</action> 23 <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/ncbi/default.kfg</action>
24 </actions> 24 </actions>
25 </install> 25 </install>
26 <readme> 26 <readme>
27 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.