Mercurial > repos > crs4 > muscle
comparison tool_dependencies.xml @ 0:ec6f5279dc01 draft
Uploaded
| author | crs4 |
|---|---|
| date | Wed, 30 Oct 2013 07:34:04 -0400 |
| parents | |
| children | 533b3b2a1e66 |
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| -1:000000000000 | 0:ec6f5279dc01 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool_dependency> | |
| 3 <package name="muscle" version="3.8.31"> | |
| 4 <install version="1.0"> | |
| 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> | |
| 27 </tool_dependency> |