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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="perl" version="5.18.1">
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4 <repository changeset_revision="f19b96171787" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="snvphyl" version="1.2">
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7 <install version="1.0">
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8 <actions>
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9 <action type="setup_perl_environment">
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10 <repository changeset_revision="f19b96171787" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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11 <package name="perl" version="5.18.1" />
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12 </repository>
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13 <package>Parallel::ForkManager</package>
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14 <package>https://cpan.metacpan.org/authors/id/S/SA/SANKO/Readonly-2.00.tar.gz</package>
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15 <package>https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz</package>
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16 <package>https://cpan.metacpan.org/authors/id/A/AJ/AJPAGE/Bio-Pipeline-Comparison-1.123050.tar.gz</package>
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17 <package>https://cpan.metacpan.org/authors/id/R/RE/REHSACK/List-MoreUtils-0.410.tar.gz</package>
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18 <package>https://cpan.metacpan.org/authors/id/T/TO/TOBYINK/Exporter-Tiny-0.042.tar.gz</package>
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19 <package>https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA/JSON-2.90.tar.gz</package>
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20 <package>https://cpan.metacpan.org/authors/id/O/OV/OVID/Test-JSON-0.11.tar.gz</package>
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21 <package>https://cpan.metacpan.org/authors/id/M/MI/MIKO/String-Util-1.24.tar.gz</package>
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22 <package>https://cpan.metacpan.org/authors/id/R/RE/REHSACK/Hash-Merge-0.200.tar.gz</package>
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23 </action>
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24
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25 <action type="change_directory">../</action>
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26 <action type="shell_command">git clone http://irida.corefacility.ca/gitlab/analysis-pipelines/snvphyl-tools.git</action>
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27 <action type="change_directory">snvphyl-tools</action>
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28 <action type="shell_command">git checkout f2396b267002ccc5696d9fecb583e000dc26fe75</action>
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29 <action type="change_directory">bcfplugins/bcftools-1.2</action>
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30 <action type="shell_command">make</action>
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31 <action type="change_directory">../..</action>
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32 <action type="move_directory_files">
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33 <source_directory>.</source_directory>
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34 <destination_directory>$INSTALL_DIR/snvphyl</destination_directory>
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35 </action>
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36
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37 <action type="set_environment">
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38 <environment_variable action="set_to" name="VCF2PSEUDO">$INSTALL_DIR/snvphyl</environment_variable>
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39 <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/snvphyl/bcfplugins/bcftools-1.2/htslib-1.2.1</environment_variable>
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40 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/snvphyl/bcfplugins/bcftools-1.2</environment_variable>
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41 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
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42 <environment_variable action="set_to" name="BCFTOOLS_PLUGINS">$INSTALL_DIR/snvphyl/bcfplugins/bcftools-1.2/plugins</environment_variable>
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43 </action>
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44
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45 </actions>
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46 </install>
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47 <readme>
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48 </readme>
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49 </package>
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50
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51
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52 </tool_dependency>
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