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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <!-- http://www.bioinformatics.babraham.ac.uk/projects/bismark/bismark_v0.7.7.tar.gz -->
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4 <package name="bowtie2" version="2.0.0-beta7">
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5 <install version="1.0">
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6 <actions>
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7 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.0.0-beta7/bowtie2-2.0.0-beta7-source.zip</action>
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8 <action type="shell_command">make</action>
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9 <action type="move_file">
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10 <source>bowtie2</source>
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11 <destination>$INSTALL_DIR/bin</destination>
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12 </action>
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13 <action type="move_file">
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14 <source>bowtie2-align</source>
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15 <destination>$INSTALL_DIR/bin</destination>
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16 </action>
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17 <action type="set_environment">
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18 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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19 </action>
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20 </actions>
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21 </install>
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22 <readme>
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23 Compiling bowtie2 requires zlib and libpthread to be present on your system.
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24 </readme>
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25 </package>
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26 <!-- We ship bismark with that wrapper, so we only need to set the PATH variable -->
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27 <package name="bismark">
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28 <install version="1.0">
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3
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29 <action type="move_file">
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30 <source>bismark</source>
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31 <destination>$INSTALL_DIR/bin</destination>
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32 </action>
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33 <action type="move_file">
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34 <source>bismark_genome_preparation</source>
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35 <destination>$INSTALL_DIR/bin</destination>
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36 </action>
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37 <action type="move_file">
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38 <source>bismark_methylation_extractor</source>
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39 <destination>$INSTALL_DIR/bin</destination>
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40 </action>
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2
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41 <action type="set_environment">
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42 <environment_variable name="PATH" action="prepend_to">./</environment_variable>
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43 </action>
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44 </actions>
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45 </install>
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46 </package>
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47 </tool_dependency>
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