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annotate tool_dependencies.xml @ 1:b8d51c1a665d

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author nilesh
date Fri, 12 Jul 2013 15:55:41 -0500
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="zlib" version="1.2.8">
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4 <install version="1.0">
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5 <actions>
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6 <action type="download_by_url">http://zlib.net/zlib-1.2.8.tar.gz</action>
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7 <action type="shell_command">./configure --prefix=$INSTALL_DIR/zlib</action>
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8 <action type="shell_command">make</action>
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9 <action type="shell_command">make install prefix=$INSTALL_DIR/zlib</action>
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10 <action type="set_environment">
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11 <environment_variable name="ZLIB_PATH" action="set_to">$INSTALL_DIR/zlib/lib</environment_variable>
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12 </action>
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13 <action type="set_environment">
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14 <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/zlib/lib</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>
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19 zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. The zlib data format is itself portable across platforms.
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20 </readme>
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21 </package>
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22 <package name="sickle" version="1.21.0">
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23 <install version="1.0">
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24 <actions>
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25 <action type="shell_command">git clone https://github.com/najoshi/sickle.git</action>
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26 <action type="shell_command">make LIBS="-L$ENV[ZLIB_PATH] -lz"</action>
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27 <action type="move_file">
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28 <source>sickle</source>
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29 <destination>$INSTALL_DIR/bin</destination>
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30 </action>
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31 <action type="set_environment">
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32 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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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 Sickle requires a C compiler; GCC or clang are recommended. Sickle relies on Heng Li's kseq.h, which is bundled with the source. It also requires zlib, which is included in this repo.
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38 </readme>
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39 </package>
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40 </tool_dependency>