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Update Orione citation. Add <citations> tag. Use package_muscle_3_8_31 from iuc.
author crs4
date Thu, 04 Jun 2015 11:34:04 -0400
parents ec6f5279dc01
children
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0:ec6f5279dc01 1:533b3b2a1e66
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <set_environment version="1.0">
4 <!-- 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.
5 Change the FASTA_MAX_SIZE variable in the installed env.sh file to adjust this limit to your needs and available resources. -->
6 <environment_variable action="set_to" name="FASTA_MAX_SIZE">100000</environment_variable>
7 </set_environment>
3 <package name="muscle" version="3.8.31"> 8 <package name="muscle" version="3.8.31">
4 <install version="1.0"> 9 <repository changeset_revision="8f20b47725d8" name="package_muscle_3_8_31" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
5 <actions>
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>
7 <!-- When compiling, need to remove the '-static' linker option from the src/mk file used by src/Makefile -->
8 <action type="shell_command">sed -i 's/-static//g' src/mk</action>
9 <action type="shell_command">make -C src/</action>
10 <action type="move_file">
11 <source>src/muscle</source>
12 <destination>$INSTALL_DIR/bin</destination>
13 </action>
14 <action type="set_environment">
15 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
16 </action>
17 <action type="set_environment">
18 <environment_variable name="FASTA_MAX_SIZE" action="set_to">100000</environment_variable>
19 </action>
20 </actions>
21 </install>
22 <readme>
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.
24 Change the FASTA_MAX_SIZE variable in the installed env.sh file to adjust this limit to your needs and available resources.
25 </readme>
26 </package> 10 </package>
27 </tool_dependency> 11 </tool_dependency>