Mercurial > repos > iuc > package_r_3_0_1_with_atlas

diff tool_dependencies.xml @ 0:4aa16d4746cb draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_1_with_atlas commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
author: iuc
date: Tue, 19 May 2015 15:01:02 -0400
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue May 19 15:01:02 2015 -0400
@@ -0,0 +1,53 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="atlas" version="3.10.1">
+        <repository changeset_revision="37ff27ea37ed" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="readline" version="6.2">
+        <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="R_3_0_1" version="3.0.1">
+        <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 changeset_revision="37ff27ea37ed" name="package_atlas_3_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="atlas" version="3.10.1" />
+                    </repository>
+                    <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="readline" version="6.2" />
+                    </repository>
+                </action>
+
+                <action language="cheetah" type="template_command">
+                    #set $cmd = './configure'
+                    #if env.get('ATLAS_LIB_DIR', False):
+                        #set $cmd += ' --with-blas="-L%s -lptf77blas -lpthread -latlas" ' % $env.ATLAS_LIB_DIR
+                    #end if
+
+                    #if env.get('READLINE_LIB_PATH', False):
+                        export LDFLAGS=-L$env.READLINE_LIB_PATH &amp;&amp;
+                        export CPPFLAGS=-I$env.READLINE_INCLUDE_PATH &amp;&amp;
+                        #set $cmd += ' --with-readline=yes '
+                    #else:
+                        #set $cmd += ' --with-readline=no '
+                    #end if
+
+                    #set $cmd += ' --enable-R-shlib  --with-x=no --libdir=%s/lib/ --bindir=%s/bin/ --datarootdir=%s/share/' % ($env.INSTALL_DIR, $env.INSTALL_DIR, $env.INSTALL_DIR)
+                    $cmd
+                </action>
+                <action type="shell_command">make</action>
+                <action type="shell_command">make install</action>
+                <action type="set_environment">
+                    <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
+                    <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
+                    <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/R/lib</environment_variable>
+                    <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
+                    <environment_variable action="set_to" name="R_PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>R is a free software environment for statistical computing and graphics. http://www.r-project.org/</readme>
+    </package>
+</tool_dependency>