Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tool_dependencies.xml @ 11:2ab2418616af draft
tool_dependencies.xml - now working, added chmod for uchime_src/mk, and changed move_file
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 30 Nov 2012 10:51:36 -0600 |
| parents | 51a065071567 |
| children |
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| 10:51a065071567 | 11:2ab2418616af |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <package name="mothur" version="1.27.0"> | 3 <package name="mothur" version="1.27"> |
| 4 <install version="1.0"> | 4 <install version="1.0"> |
| 5 <actions> | 5 <actions> |
| 6 <action type="download_by_url">http://www.mothur.org/w/images/c/cb/Mothur.1.27.0.zip</action> | 6 <action type="download_by_url">http://www.mothur.org/w/images/c/cb/Mothur.1.27.0.zip</action> |
| 7 <action type="shell_command">chmod u+x Mothur.source/uchime_src/mk</action> | |
| 7 <action type="shell_command">cd Mothur.source && make</action> | 8 <action type="shell_command">cd Mothur.source && make</action> |
| 8 <action type="move_file"> | 9 <action type="move_file"> |
| 9 <source>mothur</source> | 10 <source>Mothur.source/mothur</source> |
| 10 <destination>$INSTALL_DIR/bin</destination> | 11 <destination>$INSTALL_DIR/bin</destination> |
| 11 </action> | 12 </action> |
| 12 <action type="move_file"> | 13 <action type="move_file"> |
| 13 <source>uchime</source> | 14 <source>Mothur.source/uchime</source> |
| 14 <destination>$INSTALL_DIR/bin</destination> | 15 <destination>$INSTALL_DIR/bin</destination> |
| 15 </action> | 16 </action> |
| 16 <action type="set_environment"> | 17 <action type="set_environment"> |
| 17 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | 18 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> |
| 18 <environment_variable name="MOTHUR_MAX_PROCESSORS" action="set_to">2</environment_variable> | 19 <environment_variable name="MOTHUR_MAX_PROCESSORS" action="set_to">2</environment_variable> |