comparison tool_dependencies.xml @ 1:359b0988e735 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_ucsc_tools_0_1 commit 025696892784ba9fd07404ce4d21f3dca4ac1a1e-dirty

0:4e9561e890fe

<?xml version='1.0' encoding='utf-8'?>
<tool_dependency>
    <!-- This package will not track any version of the underlying toools.
    Any hint how to compile or ship the binaries without violating the license is very much appreciated.
    -->
    <package name="ucsc_tools" version="0.1">
        <install version="1.0">
            <actions>
                <action type="download_binary">
                    <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
                    <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
                    <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
                    <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template>
                </action>
                <action type="chmod">
                    <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
                </action>
                <action type="download_binary">
                    <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template>
                    <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
                    <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
                    <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
                </action>
                <action type="chmod">
                    <file mode="755">$INSTALL_DIR/bigWigInfo</file>
                </action>
                <action type="download_binary">
                    <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph</url_template>
                    <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
                    <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
                    <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigToBedGraph</url_template>
                </action>
                <action type="chmod">
                    <file mode="755">$INSTALL_DIR/bigWigToBedGraph</file>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                    <environment_variable name="UCSC_TOOLS_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                </action>
             </actions>
         </install>
         <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
     </package>
</tool_dependency>

1:359b0988e735

<?xml version='1.0' encoding='utf-8'?>
<tool_dependency>
    <package name="ucsc_tools" version="0.1">
        <install version="1.0">
            <actions_group>
                <actions architecture="x86_64" os="linux">
                    <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/ucsc/ucsc-312-Linux-x86_64.tar.gz</action>
                    <action type="shell_command">rm ucsc-312-Linux-x86_64.tar.gz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <!--actions architecture="x86_64" os="darwin">
                    <action type="download_by_url"></action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
                    </action>
                </actions-->
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable>
                    <environment_variable name="UCSC_TOOLS_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                </action>
            </actions_group>
         </install>
         <readme>The well known UCSC tools from Jim Kent.</readme>
     </package>
</tool_dependency>