--- a/tool_dependencies.xml	Wed Aug 05 02:50:43 2015 -0400
+++ b/tool_dependencies.xml	Tue Mar 29 07:01:13 2016 -0400
@@ -1,18 +1,49 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="sortmerna" version="2.0">
+    <package name="sortmerna" version="2.1b">
         <install version="1.0">
-            <actions>
-                <action type="download_by_url" target_filename="sortmerna-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action>
-                <action type="autoconf"/>
-                <action type="set_environment">
-                    <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR</environment_variable>
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
+            <actions_group>
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url" target_filename="sortmerna-2.1b.tar.gz">https://github.com/biocore/sortmerna/archive/2.1b.tar.gz</action>
+                    <action type="shell_command"><![CDATA[
+                        ./build.sh --prefix=$INSTALL_DIR
+                    ]]>
+                    </action>
+                    <action type="shell_command">make install</action>
+                    <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
+                    <action type="move_directory_files">
+                        <source_directory>rRNA_databases/</source_directory>
+                        <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory>
+                    </action>
+                    <action type="set_environment">
+                        <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable>
+                        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    </action>
+                </actions>
+                <actions architecture="x86_64" os="darwin">
+                    <action type="download_by_url" target_filename="sortmerna-2.1b.tar.gz">https://github.com/biocore/sortmerna/archive/2.1b.tar.gz</action>
+                    <action type="shell_command"><![CDATA[
+                        export CC=gcc-mp-4.8 && export CXX=g++-mp-4.8 && ./build.sh --prefix=$INSTALL_DIR && make install
+                    ]]>
+                    </action>
+                    <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
+                    <action type="move_directory_files">
+                        <source_directory>rRNA_databases/</source_directory>
+                        <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory>
+                    </action>
+                    <action type="set_environment">
+                        <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable>
+                        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    </action>
+                </actions>
+            </actions_group>
         </install>
         <readme>
-        SortMeRNA requires g++ 4.3 or later. Installation may take a moment since ribosomal databases have to be indexed.
+        SortMeRNA requires g++ 4.8 or later.
+
+        Note: the Clang compiler on Mac (distributed through Xcode) does not
+        support multithreading. The user is recommended to install the original
+        GCC compiler via MacPorts
         </readme>
     </package>
 </tool_dependency>