view tool_dependencies.xml @ 37:17f10d28dab3

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<?xml version="1.0"?>
<tool_dependency>
	<!-- Optimized samtools (for threaded mpileup) -->
	<package name="samtools-parallel-mpileup" version="0.1.19">
		<install version="1.0">
			<actions>
				<action type="shell_command">svn checkout https://github.com/yhoogstrate/parallel-mpileup/trunk samtools-parallel-mpileup &amp;&amp; cd samtools-parallel-mpileup &amp;&amp; cd $(ls |grep samtools-) &amp;&amp; make &amp;&amp; cp samtools ../samtools-parallel-mpileup</action>
				<action type="move_file">
					<source>samtools-parallel-mpileup</source>
					<destination>$INSTALL_DIR/bin</destination>
				</action>
				<action type="set_environment">
					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
					<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>
				</action>
			</actions>
		</install>
		<readme>
			Downloads and installs a modified version of samtools, able to paralellize the mpileup function.
		</readme>
	</package>
	
	<!-- Classical samtools (doesn't support threaded mpileup) -->
    <package name="samtools" version="0.1.19">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
                <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
                <action type="shell_command">make</action>
                <action type="shell_command">chmod ugo+rx misc/*.p?</action>
                <action type="shell_command">mkdir misc/bin</action>
                <action type="shell_command">cp -p `find misc -type f -perm -555` misc/bin/</action>
                <action type="move_file">
                    <source>samtools</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>bcftools/bcftools</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>bcftools/vcfutils.pl</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_directory_files">
                    <source_directory>misc/bin</source_directory>
                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.19 

Usage:   samtools &lt;command&gt; [options]

Command: view        SAM&lt;-&gt;BAM conversion
         sort        sort alignment file
         mpileup     multi-way pileup
         depth       compute the depth
         faidx       index/extract FASTA
         tview       text alignment viewer
         index       index alignment
         idxstats    BAM index stats (r595 or later)
         fixmate     fix mate information
         flagstat    simple stats
         calmd       recalculate MD/NM tags and '=' bases
         merge       merge sorted alignments
         rmdup       remove PCR duplicates
         reheader    replace BAM header
         cat         concatenate BAMs
         targetcut   cut fosmid regions (for fosmid pool only)
         phase       phase heterozygotes

This also installs bcftools and misc utility commands:
        bcftools
        vcfutils.pl
        ace2sam
        bamcheck
        blast2sam.pl
        bowtie2sam.pl
        export2sam.pl
        interpolate_sam.pl
        maq2sam-long
        maq2sam-short
        md5fa
        md5sum-lite
        novo2sam.pl
        psl2sam.pl
        sam2vcf.pl
        samtools.pl
        soap2sam.pl
        varfilter.py
        wgsim
        wgsim_eval.pl
        zoom2sam.pl
        </readme>
    </package>
	
	<package name="VarScan" version="2.3.6">
		<install version="1.0">
			<actions>
				<action type="download_by_url">http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar</action>
				<action type="move_file">
					<source>VarScan.v2.3.6.jar</source>
					<destination>$INSTALL_DIR/jars</destination>
				</action>
				<action type="set_environment">
					<environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
				</action>
			</actions>
		</install>
		<readme>
			Downloads VarScan2.
		</readme>
	</package>
</tool_dependency>