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annotate tool_dependencies.xml @ 11:91558de676f4

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Update to latest toolkit version - fix installation issues.
author Matt Shirley <mdshw5@gmail.com>
date Mon, 30 Mar 2015 14:06:16 -0400
parents 16f96ab0196b
children d45b5bdcff3f
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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="set_environment">
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7 <environment_variable name="NCBI" action="set_to">$PWD/ncbi</environment_variable>
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8 <environment_variable name="BUILD" action="set_to">$PWD/build</environment_variable>
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9 <environment_variable name="LD_LIBRARY_PATH" action="append_to">$INSTALL_DIR/lib64</environment_variable>
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10 <environment_variable name="LD_LIBRARY_PATH" action="append_to">$INSTALL_DIR/lib</environment_variable>
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11 </action>
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12 <action type="make_directory">$BUILD</action>
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13 <action type="make_directory">$NCBI</action>
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14 <action type="change_directory">$NCBI</action>
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15 <action type="shell_command">git clone https://github.com/ncbi/sra-tools.git</action>
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16 <action type="shell_command">git clone https://github.com/ncbi/ncbi-vdb.git</action>
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17 <action type="shell_command">git clone https://github.com/ncbi/ngs.git</action>
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18 <action type="change_directory">$NCBI/ncbi-vdb</action>
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19 <action type="shell_command">git checkout bf5ffdd</action>
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20 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$BUILD</action>
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21 <action type="change_directory">$NCBI/ngs</action>
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22 <action type="shell_command">git checkout 3a7a0ed</action>
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23 <action type="change_directory">$NCBI/ngs/ngs-sdk</action>
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24 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$BUILD</action>
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25 <action type="change_directory">$NCBI/sra-tools</action>
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26 <action type="shell_command">git checkout 4ef7ea0</action>
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27 <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$BUILD --with-ncbi-vdb-build=$BUILD --with-ncbi-vdb-sources=$NCBI/ncbi-vdb --with-ngs-sdk-prefix=$INSTALL_DIR --with-magic-prefix=/dev/null</action>
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28 <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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29 </actions>
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30 </install>
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31 <readme>
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32 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
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33 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
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34 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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35 download of a large SRA data set.
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37 Build Requirements:
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38 - make
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39 - git
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40 - gcc
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41 - g++
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42 - libxml2
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43 - libcurl4
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44 - zlib
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45
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46 On a debian based Linux OS use:
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48 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
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49
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50 </readme>
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51 </package>
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52 </tool_dependency>