comparison tool_dependencies.xml @ 0:72432392e81a draft

Uploaded tool_dependencies.xml

0:72432392e81a

<?xml version="1.0"?>
<tool_dependency>
    <package name="samtools" version="0.1.16">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.16/samtools-0.1.16.tar.bz2</action>
                <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
                <action type="shell_command">make</action>
                <action type="move_file">
                    <source>samtools</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
This is the last version of SAMTools to include the 'pileup' command.

Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.16 (r963:234)

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

Command: view        SAM&lt;-&gt;BAM conversion
         sort        sort alignment file
         pileup      generate pileup output
         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
         glfview     print GLFv3 file
         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
        </readme>
    </package>
</tool_dependency>