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annotate tool_dependencies.xml @ 16:dd337a830b5c

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Use patched versions of tools.
author Matt Shirley <mdshw5@gmail.com>
date Mon, 30 Mar 2015 16:22:27 -0400
parents c71031b17e08
children a8261e9cbe13
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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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5 <actions>
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6 <action type="make_directory">src</action>
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7 <action type="make_directory">build</action>
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8 <action type="change_directory">src</action>
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9 <action type="shell_command">git clone https://github.com/mdshw5/sra-tools.git</action>
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10 <action type="shell_command">git clone https://github.com/mdshw5/ncbi-vdb.git</action>
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11 <action type="shell_command">git clone https://github.com/mdshw5/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="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action>
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15 <action type="change_directory">../ngs</action>
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16 <action type="change_directory">ngs-sdk</action>
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17 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action>
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18 <action type="change_directory">../../sra-tools</action>
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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=$INSTALL_DIR --with-magic-prefix=/dev/null</action>
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20 <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/ncbi/default.kfg</action>
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21 </actions>
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22 </install>
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23 <readme>
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24 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
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25 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
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26 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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27 download of a large SRA data set.
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29 Build Requirements:
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30 - make
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31 - git
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32 - gcc
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33 - g++
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34 - libxml2
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35 - libcurl4
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36 - zlib
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37
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38 On a debian based Linux OS use:
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40 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
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41
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42 </readme>
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43 </package>
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44 </tool_dependency>