Mercurial > repos > bebatut > sortmerna

changeset 14:011ec5258e71 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 283fe2285a4e95f4505133fc7fa1eee96a4d274d-dirty
author bebatut
date Wed, 18 Nov 2015 09:19:17 -0500
parents 4016c1db6886
children baab049d3aff
files tool_dependencies.xml
diffstat 1 files changed, 33 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Tue Nov 17 06:00:30 2015 -0500
+++ b/tool_dependencies.xml	Wed Nov 18 09:19:17 2015 -0500
@@ -2,20 +2,39 @@
 <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="change_directory">../</action>
-                <action type="make_directory">$INSTALL_DIR/sortmerna-2.0/</action>
-                <action type="move_directory_files">
-                    <source_directory>sortmerna-2.0/</source_directory>
-                    <destination_directory>$INSTALL_DIR/sortmerna-2.0/</destination_directory>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/sortmerna-2.0/</environment_variable>
-                    <environment_variable name="PATH" action="prepend_to">$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">$INSTALL_DIR/sortmerna-2.0/</action>
+                        <action type="move_directory_files">
+                            <source_directory>sortmerna-2.0/</source_directory>
+                            <destination_directory>$INSTALL_DIR/sortmerna-2.0/</destination_directory>
+                        </action>
+                        <action type="set_environment">
+                            <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/sortmerna-2.0/</environment_variable>
+                            <environment_variable name="PATH" action="prepend_to">$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=clang && export CXX=clang++ && ./configure && make && make install
+                        ]]>
+                        </action>
+                        <action type="change_directory">../</action>
+                        <action type="make_directory">$INSTALL_DIR/sortmerna-2.0/</action>
+                        <action type="move_directory_files">
+                            <source_directory>sortmerna-2.0/</source_directory>
+                            <destination_directory>$INSTALL_DIR/sortmerna-2.0/</destination_directory>
+                        </action>
+                        <action type="set_environment">
+                            <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/sortmerna-2.0/</environment_variable>
+                            <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                        </action>                
+                    </actions>
+                </actions_group>
         </install>
         <readme>
         SortMeRNA requires g++ 4.3 or later.