No installation of diamond for MacOSX

[bebatut]

Hello,

Diamond installation from ToolShed fails on MacOSX.

It seems that installation in tool_dependencies.xml of the required packages_diamond_0_6_13 is limited to linux. Following the compilation instructions of Diamond, I suggest to change the tool_dependencies.xml of packages_diamond_0_6_13 with:

<?xml version="1.0"?>
<tool_dependency>
    <package name="diamond" version="0.6.13">
        <install version="1.0">
            <actions_group>
                <!-- Download the binaries for BLAST+ compatible with 64-bit Linux. -->
                <actions os="linux" architecture="x86_64">
                    <action type="download_by_url">http://www-ab.informatik.uni-tuebingen.de/data/software/diamond/download/public/diamond-linux64.tar.gz</action>
                    <action type="move_file">
                        <source>diamond</source>
                        <destination>$INSTALL_DIR</destination>
                    </action>
                </actions>
                <actions os="darwin" architecture="x86_64">
                    <action type="download_by_url">http://github.com/bbuchfink/diamond/archive/v0.7.9.tar.gz</action>
                    <action type="change_directory">src/</action>
                    <action type="shell_command">./install-boost</action>
                    <action type="shell_command">make</action>
                    <action type="move_file">
                        <source>../bin/diamond</source>
                        <destination>$INSTALL_DIR</destination>
                    </action>
                </actions>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                    <environment_variable name="DIAMOND_ROOT_DIR" action="set_to">$INSTALL_DIR</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme>DIAMOND is a new high-throughput program for aligning a file of short reads against a protein reference database such as NR, at 20,000 times the speed of BLASTX, with high sensitivity</readme>
    </package>
</tool_dependency>

What do you think?

I tested installation of packages_diamond_0_6_13 with a local ToolShed and it seems to work.

Thanks

[bgruening]

@bebatut as you see I have no access to an OS-X so I really appreciate your testing. This change looks good to me, but we would need to include the source of version 6.9. Do you have a link to this older version.

I will try to work on an updated version during the Metagenomic Codefest: https://github.com/galaxyproject/tools-iuc/issues/299 Do you have time to join and help me with this?

[bebatut]

I did not check the version and take the current one. The current wrapper was for version 6.9? If so, I have to check installation on MacOS. But I don't have a link to sources for 6.9 and I can't find it. Do you have one?

@bgruening I will join the codefest with the french community event organized by @yvanlebras. I will be pleased to help you with diamond

[bgruening]

I already had troubles to make this 6.9 version sustainable. So I guess an upgrade makes much sense. Looking forward to work with you on this!