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annotate tool_dependencies.xml @ 2:2c5483e80fb7 draft

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author mvdbeek
date Fri, 14 Aug 2015 12:48:14 -0400
parents 29892b1d24b9
children fb21b2e48a1e
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1 <?xml version="1.0"?>
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2 <tool_dependency>
2
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3 <package name="sra_toolkit" version="2.5.2">
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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="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
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10 <action type="shell_command">
2
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11 tar -xf 2.5.2.tar.gz
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12 rm 2.5.2.tar.gz
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13 mv sra-tools-2.5.2 sra-tools
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14 </action>
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15 <action type="download_by_url">https://github.com/ncbi/ngs/archive/1.1.3.tar.gz</action>
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16 <action type="shell_command">
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17 tar -xf 1.1.3.tar.gz
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18 rm 1.1.3.tar.gz
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19 mv ngs-1.1.3 ngs
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20 </action>
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21 <action type="download_by_url">https://github.com/ncbi/ncbi-vdb/archive/2.5.2.tar.gz</action>
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22 <action type="shell_command">
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23 tar -xf 2.5.2.tar.gz
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24 rm 2.5.2.tar.gz
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25 mv ncbi-vdb-2.5.2 ncbi-vdb
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26 </action>
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27 <action type="shell_command">
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28 LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib
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29 cd $INSTALL_DIR/src/ncbi-vdb
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30 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
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31 make
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32 make install
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33 cd $INSTALL_DIR/src/ngs/ngs-sdk
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34 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
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35 make
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36 make install
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37 cd $INSTALL_DIR/src/sra-tools
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38 ./configure --prefix=$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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39 sed -i -e "109s/-static//" tools/copycat/Makefile
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40 make
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41 make install
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42 cd $INSTALL_DIR/bin
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43 ./vdb-config -s "/repository/user/main/public/cache-enabled=false"
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44 ./vdb-config -s "/repository/user/main/public/root=$INSTALL_DIR"
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45 </action>
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46 <action type="set_environment">
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47 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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48 </action>
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49 </actions>
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50 </install>
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51 <readme>
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52 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
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53 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
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54 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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55 download of a large SRA data set.
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56
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57 Build Requirements:
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58 - make
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59 - git
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60 - gcc
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61 - g++
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62 - libxml2
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63 - libcurl4
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64 - zlib
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65
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66 On a debian based Linux OS use:
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67
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68 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
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69
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70 </readme>
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71 </package>
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72 </tool_dependency>