Mercurial > repos > matt-shirley > sra_tools
annotate tool_dependencies.xml @ 47:04cc8176e86f draft default tip
update to SRA toolkit 2.3.3-3
author | Matt Shirley <mdshw5@gmail.com> |
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date | Mon, 16 Sep 2013 20:27:28 -0400 |
parents | 88a13a2fd23f |
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tool dependencies for automated sra_sdk download and compilation
Matt Shirley <mdshw5@gmail.com>
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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"> |
19 | 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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update to SRA toolkit 2.3.3-3
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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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tool dependencies for automated sra_sdk download and compilation
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35 </readme> |
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36 </package> |
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37 </tool_dependency> |