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1 <?xml version="1.0"?>
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2 <tool_dependency>
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2
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3 <set_environment version="1.0">
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4 <environment_variable name="PERL5LIB" action="set_to">$REPOSITORY_INSTALL_DIR/perl</environment_variable>
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5 </set_environment>
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6 <package name="vcftools" version="0.1.11">
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7 <install version="1.0">
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8 <actions>
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9 <action type="download_by_url">http://downloads.sourceforge.net/project/vcftools/vcftools_0.1.11.tar.gz</action>
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10 <action type="shell_command">make</action>
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11 <action type="shell_command">PREFIX="$INSTALL_DIR/vcftools" make install</action>
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12 <!-- For some reason, the vcftools binary does not get installed using 'make install' above, so include manually. -->
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13 <action type="shell_command">cp bin/vcftools $INSTALL_DIR/vcftools/bin</action>
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14 <action type="set_environment">
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15 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/vcftools/bin</environment_variable>
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16 </action>
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2
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17 <action type="set_environment">
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18 <environment_variable name="PERL5LIB" action="prepend_to">$INSTALL_DIR/vcftools/lib/perl5/site_perl</environment_variable>
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19 </action>
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20 </actions>
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21 </install>
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22 <readme>
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23 A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project
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24 </readme>
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25 </package>
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26 </tool_dependency> |
