<?xml version="1.0"?>
<tool_dependency>
    <package name="nose" version="1.3.7">
        <repository changeset_revision="e0d81eee3c51" name="package_nose_1_3_7" owner="yhoogstrate" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    
    <package name="numpy" version="1.9">
        <repository changeset_revision="d6f39c80e75b" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    
    <package name="cython" version="0.23.1">
        <repository changeset_revision="45abfe2b0cfc" name="package_cython_0_23_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    
    <package name="crossmap" version="0.2">
        <install version="1.0">
            <actions>
                <action sha256sum="eb983c8d0ff0331f069e2378768d8988b6b9d8dd303a0f0f0cef9d882256af85" type="download_by_url">http://sourceforge.net/projects/crossmap/files/CrossMap-0.2.tar.gz</action>
                
                <action type="setup_python_environment">
                    <repository changeset_revision="e0d81eee3c51" name="package_nose_1_3_7" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="nose" version="1.3.7" />
                    </repository>
                    <repository changeset_revision="45abfe2b0cfc" name="package_cython_0_23_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="cython" version="0.23.1" />
                    </repository>
                    <repository changeset_revision="d6f39c80e75b" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="numpy" version="1.9" />
                    </repository>
                </action>
                
                <!-- CrossMap doesn't pick up the correct Cython path.
                Therefore install it with a manual shell_command instead
                of <package></package> inside a pyton_env. -->
                <action type="shell_command">
                    sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1(sig_list)/" "bin/CrossMap.py" ;
                    
                    export PYTHONPATH="$CYTHON_PATH/lib:$PYTHONPATH" &amp;&amp;
                    export PYTHONPATH="$CYTHON_PATH/lib/python:$PYTHONPATH" &amp;&amp;
                    export PYTHONPATH="$CYTHON_PATH/lib/python/Cython-0.20.1-py2.7-linux-x86_64.egg:$PYTHONPATH" &amp;&amp;
                    
                    python setup.py install --root $INSTALL_DIR
                </action>
                
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/usr/local/lib/python2.7/site-packages</environment_variable>
                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/usr/local/lib/python2.7/dist-packages</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/usr/local/bin</environment_variable>
                    
                    <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/usr/local/bin</environment_variable>
                    <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
CrossMap is versatile tool to convert genome coordinates or annotation files between genome
assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
and VCF, reading from remote servers and file compression are supported.

NEWS:
 * 08/11/15: Release version 0.2: Fixed the bug that CrossMap will not convert wiggle format files due to name collision with bx python.
 * 07/27/15: Release version 0.1.9. For VCF file conversion in v0.1.9:
  - CrossMap uses the indexed reference genome (target assembly) sequences rather than load
the entire file into memory. Users could index their reference genome file using samtools faidx
before running CrossMap, otherwise CrossMap will index it automatically the first time you run it.
  - In the output VCF file, whether the chromosome IDs contain "chr" or not depends on the input
format.
 * 05/15/15: Release version 0.1.8: Fixed the bug that CrossMap will output invalid VCF file when the
input VCF file contains a INFO field with whitespace.
 * 05/04/15: Release version 0.1.7: Address the problem that CrossMap does not convert strand in
inversions when input file is BED6 or BED12 format.
 * 11/06/14: Release version 0.1.6: Fixed "negative coordinates" bug.
 * 08/05/14: Release version 0.1.5: Support compressed (*.gz, *.Z, *.z, *.bz, *.bz2, *.bzip2) wiggle file
as input.
 * 05/19/14: add chain files for hg38-&gt;hg19, hg19-&gt;hg38, hg18-&gt;hg38, hg19-&gt;GRCh37,
GRCh37-&gt;hg19. In CrossMap v0.1.4, conversion results of BAM/SAM files can be directed to
STDOUT to support piping.
 * 12/12/13: CrossMap was accepted by Bioinformatics
 * 10/23/13: CrossMap (0.1.3) was released
 
Documentation: http://crossmap.sourceforge.net/
        </readme>
    </package>
</tool_dependency>