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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="bwa" version="0.6.2">
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4 <repository changeset_revision="0778635a84ba" name="package_bwa_0_6_2" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="blat" version="35">
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7 <!-- <repository name="package_blat_35x1" owner="iuc" /> This may be used instead of everything inside <install> when a stable Galaxy release will support the 'download_binary' action type -->
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8 </package>
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9 <package name="sequel" version="1.0.2">
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10 <install version="1.0">
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11 <actions>
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12 <action target_filename="SEQuel.tar.gz" type="download_by_url">http://bix.ucsd.edu/SEQuel/download/SEQuel.v102.tar.gz</action>
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13 <action type="move_directory_files">
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14 <source_directory>.</source_directory>
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15 <destination_directory>$INSTALL_DIR</destination_directory>
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16 </action>
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17 <action type="set_environment">
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18 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
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19 </action>
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20 <action type="set_environment">
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21 <environment_variable action="set_to" name="SEQUEL_JAR_PATH">$INSTALL_DIR</environment_variable>
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22 </action>
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23 <action type="set_environment">
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24 <environment_variable action="set_to" name="SEQUEL_SITE_OPTIONS">"-t 8 -p 8 -u 1"</environment_variable>
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25 </action>
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26 </actions>
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27 </install>
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28 <readme>
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29 Change the SEQUEL_SITE_OPTIONS variable in the installed env.sh file to adjust the number of threads to use in BWA alignment (-t) or the maximum number of threads for SEQuel (-p) or the minimum number of threads for SEQuel (-u).
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30 </readme>
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31 </package>
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32 </tool_dependency>
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