view ncbi_blast_plus/tool_dependencies.xml @ 24:5693417851ec draft

Uploaded v0.0.20pre15, try platform selection installation via shell commands.

<?xml version="1.0"?>
<tool_dependency>
    <package name="blast+" version="2.2.26+">
        <install version="1.0">
            <actions>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                </action>
		<!-- arch under Linux 32bit includes some variants like i386 and i686, so use as default -->
                <action type="shell_command">if [[ "$(uname)" == "Linux" ]]; then export FILENAME="ncbi-blast-2.2.26+-ia32-linux.tar.gz"; fi</action>
		<action type="shell_command">if [[ "$(arch)" == "x86_64" ]]; then export FILENAME="ncbi-blast-2.2.26+-x64-linux.tar.gz"; fi</action>
                <action type="shell_command">if [[ "$(uname)" == "Darwin" ]]; then export FILENAME="ncbi-blast-2.2.26+-universal-macosx.tar.gz"; fi</action>
		<!-- now download and unzip it, assuming can't use $FILENAME in the Tool Shed action? -->
		<action type="shell_command">wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME</action>
		<action type="shell_command">tar -zxvf $FILENAME</action>
                <!-- move the binaries to the installation directory which is now on the $PATH -->
                <action type="move_directory_files">
                    <source_directory>ncbi-blast-2.2.26+/bin</source_directory>
                    <destination_directory>$INSTALL_DIR</destination_directory>
                </action>
            </actions>
        </install>
        <readme>
Downloads the precompiled 32bit Linux, 64bit Linux, or Mac OS X BLAST+
binaries from the NCBI, which is faster than performing a local compliation,
avoids any issues with build dependencies, and is more reproducible between
installations as there is no variability from the compiler or library versions.

For more details, see:
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs&amp;DOC_TYPE=Download
        </readme>
    </package>
</tool_dependency>