Mercurial > repos > matt-shirley > ncbi_sra_toolkit

annotate tool_dependencies.xml @ 3:956e892b299d

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Add missing SRA datatype
author matt-shirley
date Mon, 07 Oct 2013 10:07:25 -0400
parents 293927a46697
children e724bff23fb6
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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="2.3.3-3">
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4 <install version="1.0">
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5 <actions>
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6 <action type="download_by_url">http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.3.3-3/sra_sdk-2.3.3-3.tar.gz</action>
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7 <action type="shell_command">make release</action>
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8 <action type="shell_command">make static</action>
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9 <action type="shell_command">make</action>
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10 <action type="make_directory">$INSTALL_DIR/bin</action>
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11 <action type="make_directory">$INSTALL_DIR/ncbi</action>
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12 <action type="make_directory">$INSTALL_DIR/ncbi/public</action>
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13 <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" bin64/ncbi/default.kfg</action>
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14 <action type="shell_command">cp --recursive --dereference bin64/* $INSTALL_DIR/bin</action>
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15 <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action>
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16 </actions>
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17 </install>
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18 <readme>Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
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19 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
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20 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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21 download of a large SRA data set.
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22
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23 Build Requirements:
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24 ar
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25 bash
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26 make
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27 gcc, g++
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28 libxml2
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29 libcurl4
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30 zlib
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31
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32 On a debian based Linux OS use:
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33
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34 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
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35 </readme>
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36 </package>
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37 </tool_dependency>