globalConfig.xml

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<globalConfig xmlns="globalconfig.xml.molmed">
    <programs>
        <program>
            <name>bwa</name>
	    <path>/data/programs/bwa-0.7.5a/bwa</path>
	    <version>0.7.5a</version>
        </program>
        <program>
            <name>samtools</name>
	    <path>/data/programs/samtools-0.1.19/samtools</path>
	    <version>0.1.19</version>
        </program>
        <program>
            <name>qualimap</name>
	    <path>/data/programs/qualimap_v2.2/qualimap</path>
	    <version>v2.2</version>
        </program>
	<program>
            <name>RNA-SeQC</name>
	    <path>/data/programs/RNA-SeQC_v1.1.7.jar</path>
	    <version>v1.1.7</version>
        </program>
	<program>
            <name>tophat</name>
	    <path>/data/programs/tophat-2.0.10.Linux_x86_64/tophat2</path>
	    <version>2.0.10</version>
        </program>
	<program>
            <name>cutadapt</name>
	    <path>/data/programs/cutadapt/cutadapt-1.4.1/bin/cutadapt</path>
	    <version>1.4.1</version>
        </program>
        <program>
            <name>cufflinks</name>
	    <path>/data/programs/cufflinks-2.1.1.Linux_x86_64/cufflinks</path>
	    <version>2.1.1</version>
        </program>
        <program>
            <name>cuffdiff</name>
	    <path>/data/programs/cufflinks-2.1.1.Linux_x86_64/cuffdiff</path>
	    <version>2.1.1</version>
        </program>
        <program>
            <name>fixemptyreads</name>
	    <path>/data/programs/FixEmptyReads.pl</path>
	    <version>1.0</version>
          </program>
        <program>
            <name>snpEff</name>
            <path>/data/programs/snpEff/snpEff</path>
            <version>4.0</version>
        </program>
        <program>
            <name>bcftools</name>
            <path>/data/programs/bcftools/bcftools</path>
            <version>1.2</version>
        </program>
    </programs>
    <resources>
        <resource>
            <name>dbsnp</name>
	    <path>/data/test_data/piper_references/gatk_bundle/2.8/b37/dbsnp_138.b37.vcf</path>
	    <version>gatk-bundle/2.8</version>
        </resource>
        <resource>
            <name>indels</name>
	    <path>/data/test_data/piper_references/gatk_bundle/2.8/b37/Mills_and_1000G_gold_standard.indels.b37.vcf</path>
	    <version>gatk-bundle/2.8</version>
        </resource>
        <resource>
            <name>indels</name>
	    <path>/data/test_data/piper_references/gatk_bundle/2.8/b37/1000G_phase1.indels.b37.vcf</path>
	    <version>gatk-bundle/2.8</version>
        </resource>
        <resource>
            <name>hapmap</name>
	    <path>/data/test_data/piper_references/gatk_bundle/2.8/b37/hapmap_3.3.b37.vcf</path>
	    <version>gatk-bundle/2.8</version>
        </resource>
        <resource>
            <name>omni</name>
	    <path>/data/test_data/piper_references/gatk_bundle/2.8/b37/1000G_omni2.5.b37.vcf</path>
	    <version>gatk-bundle/2.8</version>
        </resource>
        <resource>
            <name>mills</name>
	    <path>/data/test_data/piper_references/gatk_bundle/2.8/b37/Mills_and_1000G_gold_standard.indels.b37.vcf</path>
	    <version>gatk-bundle/2.8</version>
        </resource>
        <resource>
            <name>thousandGenomes</name>
	    <path>/data/test_data/piper_references/gatk_bundle/2.8/b37/1000G_phase1.snps.high_confidence.b37.vcf</path>
	    <version>gatk-bundle/2.8</version>
        </resource>
        <resource>
             <name>snpEffReference</name>
             <version>GRCh37.75</version>
             <path>/not/applicable</path>
         </resource>
    </resources>
</globalConfig>