Mercurial > repos > iuc > package_r_3_0_3

changeset 3:a8438aa1207c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_3 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
author iuc
date Fri, 17 Jul 2015 10:52:21 -0400
parents f386d7431fe0
children afc48696ee5c
files tool_dependencies.xml
diffstat 1 files changed, 31 insertions(+), 30 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Tue Jun 24 15:47:01 2014 -0400
+++ b/tool_dependencies.xml	Fri Jul 17 10:52:21 2015 -0400
@@ -1,59 +1,59 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="R" version="3.0.3">
-      <install version="1.0">
-          <actions_group>
-              <actions architecture="x86_64" os="darwin">
-                  <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/R/R-3.0.3-Darwin-x86_64.tgz</action>
+    <package name="R" version="3.0.3">
+        <install version="1.0">
+            <actions_group>
+                <actions architecture="x86_64" os="darwin">
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/R/R-3.0.3-Darwin-x86_64.tgz</action>
                     <action type="move_directory_files">
-                      <source_directory>.</source_directory>
+                        <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR</destination_directory>
                     </action>
                     <action type="shell_command">sh $INSTALL_DIR/darwin_post_install.sh $INSTALL_DIR</action>
                 </actions>
                 <actions architecture="x86_64" os="linux">
-                  <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/R/R-3.0.3-Linux-x86_64.tgz</action>
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/R/R-3.0.3-Linux-x86_64.tgz</action>
                     <action type="move_directory_files">
-                      <source_directory>.</source_directory>
+                        <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR</destination_directory>
                     </action>
                     <action type="set_environment">
-                      <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable>
+                        <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable>
                         <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable>
                     </action>
                 </actions>
                 <actions>
-                  <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 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="libpng" version="1.6.7">
-                      <repository changeset_revision="db14a391648d" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+                        <repository changeset_revision="f48b920cae1f" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                     </package>
                     <package name="cairo" version="1.12.14">
-                      <repository changeset_revision="b39299b4b6e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+                        <repository changeset_revision="b39299b4b6e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                     </package>
                     <package name="pixman" version="0.32.4">
-                      <repository changeset_revision="3d44a209a6b9" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+                        <repository changeset_revision="3d44a209a6b9" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                     </package>
                     <package name="freetype" version="2.5.2">
-                      <repository changeset_revision="58782940c411" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+                        <repository changeset_revision="58782940c411" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                     </package>
                     <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.0.3.tar.gz</action>
                     <action type="set_environment_for_install">
-                      <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
-                          <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 name="readline" version="6.2" />
                         </repository>
-                        <repository changeset_revision="db14a391648d" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
-                          <package name="libpng" version="1.6.7" />
+                        <repository changeset_revision="f48b920cae1f" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
+                            <package name="libpng" version="1.6.7" />
                         </repository>
-                        <repository changeset_revision="b39299b4b6e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
-                          <package name="cairo" version="1.12.14" />
+                        <repository changeset_revision="b39299b4b6e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
+                            <package name="cairo" version="1.12.14" />
                         </repository>
-                        <repository changeset_revision="3d44a209a6b9" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
-                          <package name="pixman" version="0.32.4" />
+                        <repository changeset_revision="3d44a209a6b9" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
+                            <package name="pixman" version="0.32.4" />
                         </repository>
-                        <repository changeset_revision="58782940c411" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
-                          <package name="freetype" version="2.5.2" />
+                        <repository changeset_revision="58782940c411" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
+                            <package name="freetype" version="2.5.2" />
                         </repository>
                     </action>
                     <action type="shell_command">
@@ -75,22 +75,23 @@
                                     --enable-R-shlib \
                                     --disable-R-framework \
                                     --libdir=$INSTALL_DIR/lib \
-                                    --prefix=$INSTALL_DIR 
+                                    --prefix=$INSTALL_DIR
                     </action>
                     <action type="make_install" />
-                    <action type="shell_command">sed -i.bak 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
-                    <action type="shell_command">sed -i.bak 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
+                    <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
+                    <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
                 </actions>
                 <action type="set_environment">
-                  <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable>
+                    <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable>
                     <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR/lib/R</environment_variable>
                     <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/lib/R/include</environment_variable>
                     <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/lib/R/share</environment_variable>
                     <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
-                    <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
+                    <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR</environment_variable>
                     <environment_variable action="set_to" name="RHOME">$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/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/R/lib</environment_variable>
                 </action>
             </actions_group>
         </install>