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10
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="spades" version="3.1.1">
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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://spades.bioinf.spbau.ru/release3.1.1/SPAdes-3.1.1-Linux.tar.gz</action>
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7 <!-- Copying the whole bin folder -->
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8 <action type="make_directory">$INSTALL_DIR/bin</action>
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9 <action type="make_directory">$INSTALL_DIR/share</action>
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10 <action type="move_directory_files">
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11 <source_directory>bin</source_directory>
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12 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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13 </action>
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14 <action type="move_directory_files">
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15 <source_directory>share</source_directory>
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16 <destination_directory>$INSTALL_DIR/share</destination_directory>
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17 </action>
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18 <!-- This is required to have spades accept .dat files -->
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19 <!-- <action type="shell_command">sed -i -e "s/\('\.fa', '\.fasta', '\.fq', '\.fastq', '\.gz'\)/\\1, '.dat'/" $INSTALL_DIR/share/spades/spades_pipeline/support.py</action> -->
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20 <!-- <action type="set_environment"> -->
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21 <!-- <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> -->
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22 <!-- </action> -->
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23 </actions>
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24 </install>
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25 <readme>
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26 This installs SPAdes 3.1.1.
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27
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28 See manual here http://spades.bioinf.spbau.ru/release3.1.1/manual.html
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29 See also here http://bioinf.spbau.ru/en/spades
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30 </readme>
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31 </package>
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32 </tool_dependency>
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33
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