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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="muscle" version="3.8.31">
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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="muscle3.8.31.tar.gz">http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz</action>
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7 <!-- When compiling, need to remove the '-static' linker option from the src/mk file used by src/Makefile -->
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8 <action type="shell_command">sed -i 's/-static//g' src/mk</action>
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9 <action type="shell_command">make -C src/</action>
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10 <action type="move_file">
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11 <source>src/muscle</source>
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12 <destination>$INSTALL_DIR/bin</destination>
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13 </action>
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14 <action type="set_environment">
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15 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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16 </action>
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17 <action type="set_environment">
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18 <environment_variable name="FASTA_MAX_SIZE" action="set_to">100000</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 MUSCLE may require a lot of memory and computation time for a medium/large input multi-FASTA file, therefore a limit on the file size is enforced by the tool.
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24 Change the FASTA_MAX_SIZE variable in the installed env.sh file to adjust this limit to your needs and available resources.
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25 </readme>
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26 </package>
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27 </tool_dependency>
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