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loud perl script
author biomonika <biomonika@psu.edu>
date Thu, 28 Aug 2014 14:44:13 -0400
parents 5b01695e449a
children
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1 <tool_dependency>
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2 <set_environment version="1.0">
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3 <environment_variable name="LINKYX_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
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4 </set_environment>
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6 <package name="samtools" version="0.1.19">
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7 <install version="1.0">
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8 <actions>
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9 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
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10 <action type="shell_command">sed -i 's/O2/O2 -fPIC/' Makefile</action>
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11 <action type="shell_command">make</action>
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12 <action type="set_environment">
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13 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
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14 <environment_variable name="SAMTOOLS" action="set_to">$INSTALL_DIR</environment_variable>
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15 </action>
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16 </actions>
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17 </install>
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18 <readme>Compiling samtools with fPIC in order to create bam.h and compiled libbam.a files</readme>
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19 </package>
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20 <package name="bioperl" version="1.6.922">
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21 <install version="1.0">
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22 <actions>
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23 <action type="setup_perl_environment">
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24 <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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25 <package name="perl" version="5.18.1" />
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26 </repository>
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27 <!-- allow downloading and installing an Perl package from cpan.org-->
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28 <package>XML::Parser</package>
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29 <package>http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz</package>
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30 <package>Bio::DB::Fasta</package>
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31 <package>File::Slurp</package>
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32 <package>Bio::DB::Sam</package>
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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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40 </tool_dependency>