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annotate 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
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="sra_toolkit" version="2.4.5">
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4 <install version="1.0">
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6 <action type="make_directory">ncbi</action>
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7 <action type="make_directory">ncbi/build</action>
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8 <action type="change_directory">ncbi</action>
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9 <action type="shell_command">git clone https://github.com/ncbi/sra-tools.git</action>
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10 <action type="shell_command">git clone https://github.com/ncbi/ncbi-vdb.git</action>
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11 <action type="shell_command">git clone https://github.com/ncbi/ngs.git</action>
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12 <action type="shell_command">LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib</action>
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13 <action type="change_directory">ncbi-vdb</action>
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14 <action type="shell_command">git checkout bf5ffdd</action>
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15 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=../build</action>
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16 <action type="change_directory">../ngs</action>
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17 <action type="shell_command">git checkout 3a7a0ed</action>
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18 <action type="change_directory">ngs-sdk</action>
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19 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=../../build</action>
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20 <action type="change_directory">../../sra-tools</action>
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21 <action type="shell_command">git checkout 4ef7ea0</action>
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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>
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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>
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24 </actions>
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25 </install>
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26 <readme>
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27 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
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28 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
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29 When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a
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30 download of a large SRA data set.
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32 Build Requirements:
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33 - make
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34 - git
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35 - gcc
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36 - g++
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37 - libxml2
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38 - libcurl4
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39 - zlib
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41 On a debian based Linux OS use:
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43 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
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45 </readme>
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46 </package>
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47 </tool_dependency>