Mercurial > repos > mvdbeek > package_sra_toolkit_2_5_2

annotate tool_dependencies.xml @ 0:d05694dbe2d4 draft

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planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
author mvdbeek
date Fri, 25 Sep 2015 09:28:29 -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="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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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 type="set_environment_for_install">
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13 <repository changeset_revision="a3f02a928f5e" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu">
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14 <package name="ncbi_vdb" version="2.5.2" />
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15 </repository>
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16 <repository changeset_revision="f530f97e76ea" name="package_ngs_sdk_1_1_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu">
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17 <package name="ngs_sdk" version="1.1.3" />
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18 </repository>
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19 </action>
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20 <action target_filename="sra-tools-2.5.2.tar.gz" type="download_file">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
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21 <action type="shell_command">tar -xf sra-tools-2.5.2.tar.gz</action>
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22 <action type="change_directory">sra-tools-2.5.2</action>
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23 <action type="shell_command">
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24 ./configure --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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25 sed -i -e "109s/-static//" tools/copycat/Makefile
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26 </action>
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27 <action type="make_install" />
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28 <action type="shell_command">
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29 $INSTALL_DIR/bin/vdb-config --restore-defaults
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30 </action>
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31 <action type="set_environment">
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32 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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33 </action>
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34 </actions>
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35 </install>
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36 <readme>
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37 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
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38 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
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39 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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40 download of a large SRA data set.
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41
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42 Build Requirements:
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43 - make
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44 - git
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45 - gcc
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46 - g++
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47 - libxml2
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48 - libcurl4
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49 - zlib
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50
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51 On a debian based Linux OS use:
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52
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53 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
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54
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55 </readme>
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56 </package>
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57 </tool_dependency>