Mercurial > repos > rnateam > sortmerna

diff tool_dependencies.xml @ 5:233da82dc31c draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8
author rnateam
date Wed, 09 Dec 2015 09:21:28 -0500
parents 42509ccf8f59
children 97f73e0566c9
line wrap: on
line diff
--- a/tool_dependencies.xml	Wed Aug 05 02:49:26 2015 -0400
+++ b/tool_dependencies.xml	Wed Dec 09 09:21:28 2015 -0500
@@ -2,17 +2,46 @@
 <tool_dependency>
     <package name="sortmerna" version="2.0">
         <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-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action>
+                        <action type="autoconf"/>
+                        <action type="change_directory">../</action>
+                        <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
+                        <action type="move_directory_files">
+                            <source_directory>sortmerna-2.0/rRNA_databases/</source_directory>
+                            <destination_directory>$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-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action>
+                        <action type="shell_command"><![CDATA[
+                            export CC=gcc-mp-4.8 && export CXX=g++-mp-4.8 && ./configure && make && make install
+                        ]]>
+                        </action>
+                        <action type="change_directory">../</action>
+                        <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action>
+                        <action type="move_directory_files">
+                            <source_directory>sortmerna-2.0/rRNA_databases/</source_directory>
+                            <destination_directory>$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>