Mercurial > repos > biomonika > test_dependency

annotate tool_dependencies.xml @ 10:66d7b41f74b1

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author biomonika <biomonika@psu.edu>
date Mon, 25 Aug 2014 14:28:57 -0400
parents 480491c2ce1c
children 0f7ae03642e3
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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">$REPOSITORY_INSTALL_DIR</environment_variable>
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4 </set_environment>
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6 <package name="samtools" version="0.1.18">
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7 <install version="1.0">
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8 <actions>
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9 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
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10 <action type="shell_command">sed -i 's/O2/O2 -fPIC/‘ Makefile</action>
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11 <action type="shell_command">make</action>
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12 <action type="move_file">
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13 <source>samtools</source>
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14 <destination>$INSTALL_DIR/bin</destination>
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15 </action>
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16 <action type="move_file">
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17 <source>libbam.a</source>
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18 <destination>$INSTALL_DIR/bin</destination>
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19 </action>
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20 <action type="move_file">
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21 <source>bam.h</source>
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22 <destination>$INSTALL_DIR/bin</destination>
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23 </action>
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24 <action type="set_environment">
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25 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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26 </action>
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27 <action type="set_environment">
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28 <environment_variable name="SAMTOOLS" action="set_to">$INSTALL_DIR/bin</environment_variable>
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29 </action>
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30 </actions>
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31 </install>
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32 <readme>Compiling samtools with fPIC in order to create bam.h and compiled libbam.a files</readme>
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33 </package>