annotate tool_dependencies.xml @ 1:fd1537dcbe4a draft

Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.18.

<?xml version="1.0"?>
<tool_dependency>
    <package name="samtools" version="0.1.18">
        <install version="1.0">
            <actions_group>
                <actions os="linux" architecture="i386">
                    <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.18-linux-i386.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <actions os="linux" architecture="x86_64">
                    <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.18-linux-x86_64.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <actions os="darwin" architecture="i386">
                    <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.18-Darwin-i386.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <actions os="darwin" architecture="x86_64">
                    <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.18-Darwin-x86_64.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <actions>
                    <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.18.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>$INSTALL_DIR/bin</destination>
                    </action>
                    <action type="move_file">
                        <source>libbam.a</source>
                        <destination>$INSTALL_DIR/lib</destination>
                    </action>
                </actions>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme>
Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.18 (r982:295)

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
        </readme>
    </package>
</tool_dependency>