Mercurial > repos > jjohnson > mothur_toolsuite

changeset 34:1be61ceb20d7

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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 d53b9eb16c2d
children 95d75b35e4d2
files mothur/tool_dependencies.xml
diffstat 1 files changed, 6 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- a/mothur/tool_dependencies.xml	Wed Sep 11 16:56:31 2013 -0500
+++ b/mothur/tool_dependencies.xml	Mon Sep 22 11:19:09 2014 -0400
@@ -4,6 +4,12 @@
         <install version="1.0">
             <actions>
                 <action type="download_by_url">http://www.mothur.org/w/images/c/cb/Mothur.1.27.0.zip</action>
+		<!-- Update the makefile -->
+		<action type="shell_command">sed -i 's/^USECOMPRESSION ?= no/USECOMPRESSION ?= yes/' Mothur.source/makefile</action>
+		<action type="shell_command">sed -i 's/TARGET_ARCH += -arch x86_64/#TARGET_ARCH += -arch x86_64/' Mothur.source/makefile</action>
+		<action type="shell_command">sed -i 's/#CXXFLAGS +=/CXXFLAGS +=/' Mothur.source/makefile</action>
+		<!-- Update the uchime_src/mk -->
+		<action type="shell_command">sed -i 's/LINK_OPTS=-static/LINK_OPTS=/' Mothur.source/uchime_src/mk</action>
                 <action type="shell_command">chmod u+x Mothur.source/uchime_src/mk</action>
                 <action type="shell_command">cd Mothur.source &amp;&amp; make</action>
                 <action type="move_file">