Mercurial > repos > rnateam > sortmerna

diff tool_dependencies.xml @ 6:97f73e0566c9 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
author rnateam
date Tue, 29 Mar 2016 06:53:28 -0400
parents 233da82dc31c
children
line wrap: on
line diff
--- a/tool_dependencies.xml	Wed Dec 09 09:21:28 2015 -0500
+++ b/tool_dependencies.xml	Tue Mar 29 06:53:28 2016 -0400
@@ -1,46 +1,48 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="sortmerna" version="2.0">
+    <package name="sortmerna" version="2.1b">
         <install version="1.0">
             <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>
+                    <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">$INSTALL_DIR/bin</environment_variable>
+                    </action>
+                </actions>
                 <actions architecture="x86_64" os="darwin">
-                        <action type="download_by_url" target_filename="sortmerna-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action>
-                        <action type="shell_command"><![CDATA[
-                            export CC=gcc-mp-4.8 && export CXX=g++-mp-4.8 && ./configure && make && make install
-                        ]]>
-                        </action>
-                        <action type="change_directory">../</action>
-                        <action type="make_directory">$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">$INSTALL_DIR/bin</environment_variable>
-                        </action>                
-                    </actions>
-                </actions_group>
+                    <action type="download_by_url" target_filename="sortmerna-2.1b.tar.gz">https://github.com/biocore/sortmerna/archive/2.1b.tar.gz</action>
+                    <action type="shell_command"><![CDATA[
+                        export CC=gcc-mp-4.8 && export CXX=g++-mp-4.8 && ./build.sh --prefix=$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++ 4.8 or later. 
+        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 
+        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>