Mercurial > repos > mvdbeek > package_sra_tools_2_5_2

annotate tool_dependencies.xml @ 0:ce7da2f8d213 draft

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author mvdbeek
date Sat, 15 Aug 2015 09:33:08 -0400
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="ncbi_vdb" version="2.5.2">
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4 <repository changeset_revision="a3f02a928f5e" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="ncbi_ngs" version="1.1.3">
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7 <repository changeset_revision="f090c319428b" name="package_ngs_1_1_3" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="sra_toolkit" version="2.5.2">
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10 <install version="1.0">
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11 <actions>
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12 <action target_filename="sra-tools-2.5.2.tar.gz" type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
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13 <action type="shell_command">
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14 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
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15 sed -i -e "109s/-static//" tools/copycat/Makefile
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16 make
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17 make install
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18 cd $INSTALL_DIR/bin
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19 ./vdb-config -s "/repository/user/main/public/cache-enabled=false"
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20 ./vdb-config -s "/repository/user/main/public/root=$INSTALL_DIR"
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21 </action>
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22 <action type="set_environment">
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23 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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24 </action>
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25 </actions>
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26 </install>
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27 <readme>
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28 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
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29 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
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30 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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31 download of a large SRA data set.
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32
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33 Build Requirements:
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34 - make
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35 - git
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36 - gcc
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37 - g++
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38 - libxml2
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39 - libcurl4
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40 - zlib
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41
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42 On a debian based Linux OS use:
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43
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44 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
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45
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46 </readme>
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47 </package>
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48 </tool_dependency>