Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tool_dependencies.xml @ 34:1be61ceb20d7
Updated tool_dependencies.xml to build mothur package on Linux (may break other OSes).
| author | pjbriggs |
|---|---|
| date | Mon, 22 Sep 2014 11:19:09 -0400 |
| parents | 49058b1f8d3f |
| children | 95d75b35e4d2 |
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| 33:d53b9eb16c2d | 34:1be61ceb20d7 |
|---|---|
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <package name="mothur" version="1.27"> | 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 <!-- Update the makefile --> | |
| 8 <action type="shell_command">sed -i 's/^USECOMPRESSION ?= no/USECOMPRESSION ?= yes/' Mothur.source/makefile</action> | |
| 9 <action type="shell_command">sed -i 's/TARGET_ARCH += -arch x86_64/#TARGET_ARCH += -arch x86_64/' Mothur.source/makefile</action> | |
| 10 <action type="shell_command">sed -i 's/#CXXFLAGS +=/CXXFLAGS +=/' Mothur.source/makefile</action> | |
| 11 <!-- Update the uchime_src/mk --> | |
| 12 <action type="shell_command">sed -i 's/LINK_OPTS=-static/LINK_OPTS=/' Mothur.source/uchime_src/mk</action> | |
| 7 <action type="shell_command">chmod u+x Mothur.source/uchime_src/mk</action> | 13 <action type="shell_command">chmod u+x Mothur.source/uchime_src/mk</action> |
| 8 <action type="shell_command">cd Mothur.source && make</action> | 14 <action type="shell_command">cd Mothur.source && make</action> |
| 9 <action type="move_file"> | 15 <action type="move_file"> |
| 10 <source>Mothur.source/mothur</source> | 16 <source>Mothur.source/mothur</source> |
| 11 <destination>$INSTALL_DIR/bin</destination> | 17 <destination>$INSTALL_DIR/bin</destination> |