view tools/spades_2_5/tool_dependencies.xml @ 3:d82f18c76309 draft

Uploaded spades wrapper 0.6. Supports spades 2.5.1. Also removes the need for the hack at installation time, by fixing the problem with input files. Shows the license for the tool as well.

<?xml version="1.0"?>
<tool_dependency>
    <package name="spades" version="2.5.0">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://spades.bioinf.spbau.ru/release2.5.1/SPAdes-2.5.1-Linux.tar.gz</action>
                <!-- Copying the whole bin folder -->
		<action type="make_directory">$INSTALL_DIR/bin</action>
		<action type="make_directory">$INSTALL_DIR/share</action>
		<action type="move_directory_files">
		  <source_directory>bin</source_directory>
		  <destination_directory>$INSTALL_DIR/bin</destination_directory>
		</action>
                <action type="move_directory_files">
		  <source_directory>share</source_directory>
		  <destination_directory>$INSTALL_DIR/share</destination_directory>
		</action>
		<!-- This is required to have spades accept .dat files -->
		<!-- <action type="shell_command">sed -i -e "s/\('\.fa', '\.fasta', '\.fq', '\.fastq', '\.gz'\)/\\1, '.dat'/" $INSTALL_DIR/share/spades/spades_pipeline/support.py</action> -->
                <!-- <action type="set_environment"> -->
                <!--     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> -->
                <!-- </action> -->
            </actions>
        </install>
        <readme>
This installs SPAdes 2.5.1.

See manual here http://spades.bioinf.spbau.ru/release2.5.1/manual.html
See also here http://bioinf.spbau.ru/en/spades
        </readme>
    </package>
</tool_dependency>