changeset 10:79759fdec6cb draft

Uploaded v0.0.2 preview 2, attempt auto-install for 64 bit Mac OS X.

--- a/tools/mira4/mira4_bait.xml	Thu Nov 28 05:07:59 2013 -0500
+++ b/tools/mira4/mira4_bait.xml	Tue Dec 10 06:26:19 2013 -0500
@@ -47,7 +47,7 @@
             <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
             <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" />
             <output name="output_reads" file="tvc_mini_bait_pos.fastq" ftype="fastqsanger" />
-	</test>
+        </test>
         <test>
             <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
             <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" />

--- a/tools/mira4/tool_dependencies.xml	Thu Nov 28 05:07:59 2013 -0500
+++ b/tools/mira4/tool_dependencies.xml	Tue Dec 10 06:26:19 2013 -0500
@@ -5,21 +5,45 @@
     </package>
     <package name="MIRA" version="4.0">
         <install version="1.0">
-            <actions>
-                <action type="download_by_url">https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0rc4_linux-gnu_x86_64_static.tar.bz2</action>
-                <action type="move_directory_files">
-                    <source_directory>bin</source_directory>
-                    <destination_directory>$INSTALL_DIR</destination_directory>
+            <actions_group>
+                <!-- Download the binaries for MIRA compatible with 64-bit OSX. -->
+                <actions architecture="x86_64" os="darwin">
+                    <action type="download_by_url">https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0rc5_darwin13.0.0_x86_64_static.tar.bz2</action>
+                    <action type="move_directory_files">
+                         <source_directory>bin</source_directory>
+                         <destination_directory>$INSTALL_DIR</destination_directory>
+                     </action>
+                </actions>
+                <!-- Download the binaries for MIRA compatible with 64-bit Linux. -->
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url">https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0rc4_linux-gnu_x86_64_static.tar.bz2</action>
+                    <action type="move_directory_files">
+                        <source_directory>bin</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>
+                </actions>
+                <!-- This actions tag is only processed if none of the above tags resulted in a successful installation. -->
+                <actions>
+                    <action type="shell_command">echo ERROR: Automated installation on your operating system and CPU architecture combination is not yet supported.</action>
+                    <action type="shell_command">echo Your machine details (the output from 'uname' and 'arch'):</action>
+                    <action type="shell_command">uname</action>
+                    <action type="shell_command">arch</action>
+                    <action type="shell_command">echo If pre-compiled MIRA binaries are now available for this, please report this</action>
+                    <action type="shell_command">echo via https://github.com/peterjc/pico_galaxyt/issues - thank you!</action>
+                    <action type="shell_command">false</action>
+                    <!-- The 'false' command will return an error, so Galaxy should treat this as a failed install -->
+                </actions>
+                <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. -->
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
                 </action>
-                <action type="set_environment">
-                    <environment_variable action="set_to" name="MIRA4">$INSTALL_DIR</environment_variable>
-                </action>
-            </actions>
+            </actions_group>
         </install>
         <readme>
 Downloads MIRA v4.0 from Sourceforge, requesting Bastien's precompiled binaries
-for 64bit Linux (x86_64). He also has binaries for Mac OS X, which we could
-use once the extensions to allow that are in the stable Galaxy releases.
+for 64 bit (x86_64) Linux or Mac OS X. Other platforms were compilation from
+source would be required (e.g. 32 bit Linux and Mac) are not supported by this
+automated installation script.
 
 http://chevreux.org/projects_mira.html
 http://sourceforge.net/projects/mira-assembler/