annotate tool_dependencies.xml @ 0:e109f0ec22c3 draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/packages/package_ascp_3 commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty

<?xml version="1.0"?>
<tool_dependency>
    <package name="ascp" version="3">
        <install version="1.0">
            <actions_group>
                <actions architecture="x86_64" os="darwin">
                    <!-- <action type="download_by_url">http://download.asperasoft.com/download/sw/connect/3.6.0/AsperaConnectInstaller-3.6.0.106805.dmg</action> -->
                    <action type="download_by_url">https://bitbucket.org/mvdbeek/galaxy_downloads/downloads/AsperaConnectInstaller-3.6.0.106805.dmg</action>
                    <action type="shell_command">hdiutil attach -mountpoint install AsperaConnectInstaller-3.6.0.106805.dmg</action>
                    <action type="shell_command">pkgutil --expand install/AsperaConnectInstaller.pkg extract</action>
                    <action type="shell_command">cat extract/AsperaConnect.pkg/Payload | gzip -d - | cpio -id</action>
                    <action type="shell_command">hdiutil detach install</action>
                    <action type="move_directory_files">
                        <source_directory>Applications/Aspera Connect.app/Contents/Resources/</source_directory>
                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
                    </action>
                    <action type="set_environment">
                        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                    </action>
                </actions>
                <actions architecture="x86_64" os="linux">
                    <!-- <action type="download_file">http://download.asperasoft.com/download/sw/ascp-client/3.5.4/ascp-install-3.5.4.102989-linux-64.sh</action> -->
                    <action type="download_file">https://bitbucket.org/mvdbeek/galaxy_downloads/downloads/ascp-install-3.5.4.102989-linux-64.sh</action>
                    <action type="download_file">https://bitbucket.org/mvdbeek/galaxy_downloads/downloads/asperaweb_id_dsa.openssh</action>
                    <action type="move_file">
                        <source>asperaweb_id_dsa.openssh</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                    <action type="shell_command">
                        sed -i.bak -e 's|if test `id -u` -ne 0; then echo You must be root; exit 1; fi||' ascp-install-3.5.4.102989-linux-64.sh
                        sed -i.bak -e 's|/usr/local|$INSTALL_DIR|'g ascp-install-3.5.4.102989-linux-64.sh
                        sed -i.bak -e 's|ln -sf $INSTALL_DIR/bin/ascp /usr/bin||' ascp-install-3.5.4.102989-linux-64.sh
                        sh ascp-install-3.5.4.102989-linux-64.sh
                    </action>
                    <action type="set_environment">
                        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                    </action>
                </actions>
            </actions_group>
        </install>

        <readme>
            This tool dependency definition downloads and installs the aspera connect client, used for accelerating
            ncbi sra downloads.
        </readme>
    </package>
</tool_dependency>