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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="sspace" version="2.0">
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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" target_filename="SSPACE-BASIC-2.0_linux-x86_64.zip">http://www.baseclear.com/download.php?file_id=1038</action>
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7 <!-- fix for Perl >= 5.16.0-->
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8 <action type="shell_command">sed -i -e 's/require "getopts.pl"/use Getopt::Std/' -e 's/&Getopts/getopts/' SSPACE_Basic_v2.0.pl</action>
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9 <action type="move_directory_files">
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10 <source_directory>.</source_directory>
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11 <destination_directory>$INSTALL_DIR</destination_directory>
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12 </action>
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13 <action type="set_environment">
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14 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
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15 </action>
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16 <action type="set_environment">
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17 <environment_variable name="SSPACE_SITE_OPTIONS" action="set_to">"-T 1"</environment_variable>
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18 </action>
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19 </actions>
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20 </install>
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21 <readme>
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22 Change the SSPACE_SITE_OPTIONS variable in the installed env.sh file to adjust the number of threads to use in Bowtie alignment (-T).
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23 </readme>
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24 </package>
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25 </tool_dependency>
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