Mercurial > repos > s-kaufmann > synteny_mapper

changeset 12:3d74b350ec59 draft

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Uploaded
author s-kaufmann
date Fri, 15 Aug 2014 09:43:10 -0400
parents 833d7d8ce458
children 25ec18816c91
files tool_dependencies.xml
diffstat 1 files changed, 27 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Fri Aug 15 09:21:02 2014 -0400
+++ b/tool_dependencies.xml	Fri Aug 15 09:43:10 2014 -0400
@@ -27,19 +27,38 @@
         </readme>
     </package>  
 
- <package name="R_3_0_1" version="3.0.1">
+    <set_environment version="1.0">
+	<environment_variable name="R_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
+<package name="readline" version="6.2">
+        <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="ncurses" version="5.9">
+        <repository changeset_revision="9ed7af129bd3" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="libpng" version="1.6.7">
+        <repository changeset_revision="51f77dcf27bd" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="R_3_0_2" version="3.0.2">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.1.tar.gz</action>
-                <!--<action type="set_environment_for_install">
-                    <repository name="package_readline_6_2" owner="iuc">
+                <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.2.tar.gz</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
                         <package name="readline" version="6.2" />
                     </repository>
-                </action>-->
+                    <repository changeset_revision="9ed7af129bd3" name="package_ncurses_5_9" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                        <package name="ncurses" version="5.9" />
+                    </repository>
+                    <repository changeset_revision="51f77dcf27bd" name="package_libpng_1_6_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu">
+                        <package name="libpng" version="1.6.7" />
+                    </repository>
+                </action>
 
-                <action type="shell_command">
-                    ./configure --with-readline=no --enable-R-shlib  --with-x=no --libdir=$INSTALL_DIR/lib/ --bindir=$INSTALL_DIR/bin/ --datarootdir=$INSTALL_DIR/share/
+<action type="shell_command">
+                    ./configure CPPFLAGS="-I$READLINE_INCLUDE_PATH -I${LIBPNG_ROOT}/include" LDFLAGS="-L$READLINE_LIB_PATH -L$NCURSES_LIB_PATH -L${LIBPNG_ROOT}/lib -lreadline -lncurses" --with-libpng --enable-R-shlib  --with-x=no --libdir=$INSTALL_DIR/lib/ --bindir=$INSTALL_DIR --datarootdir=$INSTALL_DIR/share/
                 </action>
+
                 <action type="shell_command">make</action>
                 <action type="shell_command">make install</action>
                 <action type="set_environment">
@@ -53,6 +72,6 @@
             </actions>
         </install>
         <readme>R is a free software environment for statistical computing and graphics. http://www.r-project.org/</readme>
-    </package>    
+    </package>
 
 </tool_dependency>