Mercurial > repos > matt-shirley > ncbi_sra_toolkit

annotate tool_dependencies.xml @ 26:7d80b2b24270

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Set config values for caching.
author Matt Shirley <mdshw5@gmail.com>
date Mon, 30 Mar 2015 22:11:38 -0400
parents 393a04ec0fa9
children
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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">
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10 git clone https://github.com/mdshw5/sra-tools.git
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11 git clone https://github.com/mdshw5/ncbi-vdb.git
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12 git clone https://github.com/mdshw5/ngs.git
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13 LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib
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14 cd $INSTALL_DIR/src/ncbi-vdb
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15 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
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16 make
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17 make install
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18 cd $INSTALL_DIR/src/ngs/ngs-sdk
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19 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
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20 make
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21 make install
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22 cd $INSTALL_DIR/src/sra-tools
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23 ./configure --prefix=$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
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24 make
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25 make install
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26 cd $INSTALL_DIR/bin
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27 ./vdb-config -s "/repository/user/main/public/cache-enabled=false"
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28 ./vdb-config -s "/repository/user/main/public/root=$INSTALL_DIR"
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29 </action>
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30 <action type="set_environment">
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31 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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32 </action>
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33 </actions>
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34 </install>
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35 <readme>
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36 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
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37 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
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38 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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39 download of a large SRA data set.
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41 Build Requirements:
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42 - make
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43 - git
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44 - gcc
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45 - g++
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46 - libxml2
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47 - libcurl4
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48 - zlib
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49
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50 On a debian based Linux OS use:
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52 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
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53
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54 </readme>
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55 </package>
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56 </tool_dependency>