changeset 8:b614a5abf31c draft default tip

planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/packages/package_mira_4_9_5 commit fd979d17340cde155de176604744831d9597c6b6

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu May 18 13:38:13 2017 -0400
@@ -0,0 +1,61 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="MIRA" version="4.9.5">
+        <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">
+                         <source_directory>bin</source_directory>
+                         <destination_directory>$INSTALL_DIR</destination_directory>
+                     </action>
+                </actions>
+                -->
+                <!-- Download the binaries for MIRA compatible with 64-bit Linux. -->
+                <actions architecture="x86_64" os="linux">
+                    <!-- http://downloads.sourceforge.net/project/mira-assembler/MIRA/development/mira_4.9.5_2_linux-gnu_x86_64_static.tar.bz2 -->
+                    <action type="download_by_url" sha256sum="3848885cb041cd9bf7aa8f220dd3f084443f5060fa433b669f7d28880ba4c61f">https://depot.galaxyproject.org/software/mira/mira_4.9.5_linux_x64.tar.bz2</action>
+                    <action type="move_directory_files">
+                        <source_directory>bin</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </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/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>
+                <!-- 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>
+                <!-- 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">$INSTALL_DIR/</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme>
+Downloads MIRA v4.9.5 from Sourceforge, requesting Bastien's precompiled binaries
+for 64 bit (x86_64) Linux. Currently the Mac OS X binaries are not available.
+
+Other platforms where compilation from source would be required (e.g. 32 bit Linux)
+are not supported by this automated installation script.
+
+http://chevreux.org/projects_mira.html
+http://sourceforge.net/projects/mira-assembler/
+
+The environment variable ``$MIRA4_9`` will point to the folder containing the
+binaries (with a trailing slash), and this is also pre-pended to the``$PATH``
+variable.
+        </readme>
+    </package>
+</tool_dependency>