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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="mummer" version="3.23">
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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://sourceforge.net/projects/mummer/files/mummer/3.23/MUMmer3.23.tar.gz</action>
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7 <action type="move_directory_files">
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8 <source_directory>.</source_directory>
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9 <destination_directory>$INSTALL_DIR</destination_directory>
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10 </action>
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11 <action type="shell_command">
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12 cd $INSTALL_DIR; make;
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13 </action>
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14 <action type="set_environment">
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15 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable>
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16 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
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17 </action>
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18 </actions>
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19 </install>
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20 <readme>
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21 http://mummer.sourceforge.net/
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22 MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences.
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23 </readme>
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24 </package>
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25 </tool_dependency>
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