changeset 3:4eaac2545faa draft default tip

MIRA 4.9.5 not on sourceforge anymore

--- a/tool_dependencies.xml	Wed Sep 02 06:47:20 2015 -0400
+++ b/tool_dependencies.xml	Mon Aug 08 13:02:16 2016 -0400
@@ -4,6 +4,7 @@
         <install version="1.0">
             <actions_group>
                 <!-- Download the binaries for MIRA compatible with 64-bit OSX. -->
+                <!-- Currently unavailable...
                 <actions architecture="x86_64" os="darwin">
                     <action type="download_by_url">http://downloads.sourceforge.net/project/mira-assembler/MIRA/development/mira_4.9.5_2_darwin14.3.0_x86_64_static.tar.bz2</action>
                     <action type="move_directory_files">
@@ -11,9 +12,10 @@
                          <destination_directory>$INSTALL_DIR</destination_directory>
                      </action>
                 </actions>
+                -->
                 <!-- Download the binaries for MIRA compatible with 64-bit Linux. -->
                 <actions architecture="x86_64" os="linux">
-                    <action type="download_by_url">http://downloads.sourceforge.net/project/mira-assembler/MIRA/development/mira_4.9.5_2_linux-gnu_x86_64_static.tar.bz2</action>
+                    <action type="download_by_url" sha256sum="3848885cb041cd9bf7aa8f220dd3f084443f5060fa433b669f7d28880ba4c61f">https://depot.galaxyproject.org/software/mira/mira_4.9.5_linux_x64.tar.bz2</action>
                     <action type="move_directory_files">
                         <source_directory>bin</source_directory>
                         <destination_directory>$INSTALL_DIR</destination_directory>
@@ -26,7 +28,7 @@
                     <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_galaxy/issues - thank you!"</action>
+                    <action type="shell_command">echo "via https://github.com/peterjc/galaxy_mira/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>
@@ -34,7 +36,7 @@
                 <action type="set_environment">
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
                 </action>
-                <!-- Wrapper requires trailing slash on $MIRA4_9 so make sure there is one (double trailing slash is harmless) -->
+                <!-- Note we append a trailing slash as currently expected by the wrapper XML file -->
                 <action type="set_environment">
                     <environment_variable action="set_to" name="MIRA4_9">$INSTALL_DIR/</environment_variable>
                 </action>
@@ -42,15 +44,17 @@
         </install>
         <readme>
 Downloads MIRA v4.9.5 from Sourceforge, requesting Bastien's precompiled binaries
-for 64 bit (x86_64) Linux or Mac OS X. Other platforms where compilation from
-source would be required (e.g. 32 bit Linux) are not supported by this automated
-installation script.
+for 64 bit (x86_64) Linux. Currently the Mac OS X binaries are not available.
+
+Other platforms where compilation from source would be required (e.g. 32 bit Linux)
+are not supported by this automated installation script.
 
 http://chevreux.org/projects_mira.html
 http://sourceforge.net/projects/mira-assembler/
 
 The environment variable ``$MIRA4_9`` will point to the folder containing the
-binaries, which is also pre-pended to the``$PATH`` variable.
+binaries (with a trailing slash), and this is also pre-pended to the``$PATH``
+variable.
         </readme>
     </package>
 </tool_dependency>