annotate tool_dependencies.xml @ 0:7dd0c6a9be41 draft default tip

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty

<?xml version="1.0"?>
<tool_dependency>
    <package name="ncurses" version="6.0">
        <repository changeset_revision="c921f7ce9ca7" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    
    <package name="samtools_parallel_mpileup" version="0.1.19-a">
        <install version="1.0">
            <actions>
                <action type="set_environment_for_install">
                    <repository changeset_revision="c921f7ce9ca7" name="package_ncurses_6_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="ncurses" version="6.0" />
                    </repository>
                </action>
                
                <action type="shell_command">
                    svn checkout https://github.com/yhoogstrate/parallel-mpileup/trunk samtools-parallel-mpileup ;
                    
                    cd samtools-parallel-mpileup ;
                    cd $(ls |grep samtools-) ;
                    
                    sed -i 's/-lcurses/-lncurses/' Makefile ;
                    sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile ;
                    
                    make ;
                    cp samtools ../samtools-parallel-mpileup
                </action>
                <action type="move_file">
                    <source>samtools-parallel-mpileup/samtools-parallel-mpileup</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            Downloads and installs a modified version of samtools, able to paralellize the mpileup function.
            
            *Because of the parallelization, the output is not sorted on genomic location!!*
            
            If this is required for the tool that uses the mpileup as input, sort the mpileup file with:
            
            sort -k1,1V -k2,2g
        </readme>
    </package>
</tool_dependency>