Mercurial > repos > mvdbeek > package_sra_toolkit_2_5_2

annotate tool_dependencies.xml @ 2:b7385e84a15b draft

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author mvdbeek
date Fri, 25 Sep 2015 11:31:58 -0400
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="ascp" version="3">
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4 <repository changeset_revision="e053dbdb5302" name="package_ascp_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="ncbi_vdb" version="2.5.2">
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7 <repository changeset_revision="96c348976275" name="package_ncbi_vdb_2_5_2" 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="set_environment_for_install">
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14 <repository changeset_revision="96c348976275" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu">
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15 <package name="ncbi_vdb" version="2.5.2" />
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16 </repository>
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17 <repository changeset_revision="b0e9867f0dfb" name="package_ngs_sdk_1_1_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu">
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18 <package name="ngs_sdk" version="1.1.3" />
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19 </repository>
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20 </action>
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21 <action type="autoconf">
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22 --prefix=$INSTALL_DIR -with-ngs-sdk-prefix=$NGS_SDK_DIR --with-ncbi-vdb-sources=$NCBI_VDB_DIR --with-ncbi-vdb-build=$NCBI_VDB_DIR --build=$INSTALL_DIR/build
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23 </action>
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24 <action type="shell_command">sed -i -e "109s/-static//" tools/copycat/Makefile</action>
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25 <action type="make_install" />
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26 <action type="set_environment">
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27 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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28 </action>
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29 </actions>
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30 </install>
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31 <readme>
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32 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
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33 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
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34 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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35 download of a large SRA data set.
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36
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37 Build Requirements:
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38 - make
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39 - git
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40 - gcc
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41 - g++
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42 - libxml2
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43 - libcurl4
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44 - zlib
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45
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46 On a debian based Linux OS use:
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48 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
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49
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50 </readme>
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51 </package>
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52 </tool_dependency>