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2
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1 <?xml version="1.0"?>
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0
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2 <tool_dependency>
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2
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3
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0
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4 <set_environment version="1.0">
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2
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5 <environment_variable action="set_to" name="LINKYX_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
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0
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6 </set_environment>
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7
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2
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8 <package name="perl" version="5.18.1">
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9 <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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10 </package>
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2
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11
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12 <package name="samtools-fpic" version="0.1.19">
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13 <repository changeset_revision="a6c82a5d0b51" name="package_samtools_0_1_19_custom" owner="biomonika" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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14 </package>
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15
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0
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16 <package name="bioperl" version="1.6.922">
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17 <install version="1.0">
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18 <actions>
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19 <action type="setup_perl_environment">
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2
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20 <repository changeset_revision="a6c82a5d0b51" name="package_samtools_0_1_19_custom" owner="biomonika" toolshed="https://toolshed.g2.bx.psu.edu">
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21 <package name="samtools-fpic" version="0.1.19" />
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22 </repository>
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23 <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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24 <package name="perl" version="5.18.1" />
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25 </repository>
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2
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26 <!-- allow downloading and installing an Perl package from cpan.org-->
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27 <package>XML::Parser</package>
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28 <package>http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz</package>
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29 <package>Bio::DB::Fasta</package>
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30 <package>File::Slurp</package>
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31 <package>Bio::DB::Sam</package>
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32 <package>PerlIO::gzip</package>
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0
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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 Bundle::BioPerl
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38 </readme>
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39 </package>
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2
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40 </tool_dependency>
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