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annotate tool_dependencies.xml @ 16:76917da4e1ac

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author biomonika <biomonika@psu.edu>
date Mon, 25 Aug 2014 15:12:47 -0400
parents 9c08f9866ce6
children 5bd4a63cba10
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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">$REPOSITORY_INSTALL_DIR</environment_variable>
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4 </set_environment>
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6 <package name="samtools" version="0.1.19">
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7 <install version="1.0">
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8 <actions>
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9 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
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10 <action type="shell_command">sed -i .bak -e 's/O2/O2 -fPIC/' Makefile</action>
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11 <action type="shell_command">make</action>
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12 <action type="set_environment">
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13 <environment_variable name="PATH" action="prepend_to">$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 </tool_dependency>