uppmax_global_config.xml

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<globalConfig xmlns="globalconfig.xml.molmed">
    <programs>
        <program>
            <name>bwa</name>
            <path>/sw/apps/bioinfo/bwa/0.7.12/milou/bin/bwa</path>
	    <version>0.7.12</version>
        </program>
        <program>
            <name>samtools</name>
	    <path>/sw/apps/bioinfo/samtools/0.1.19/milou/bin/samtools</path>
	    <version>0.1.19</version>	   
        </program>
        <program>
            <name>qualimap</name>
	    <path>/proj/a2014205/piper_resources/programs/qualimap_v2.0/qualimap</path>
	    <version>v2.0</version>
        </program>
	<program>
            <name>RNA-SeQC</name>
	    <path>/proj/a2014205/piper_resources/programs/RNA-SeQC_v1.1.7.jar</path>
	    <version>v1.1.7</version>
        </program>
	<program>
            <name>tophat</name>
	    <path>/sw/apps/bioinfo/tophat/2.0.10/kalkyl/bin/tophat2</path>
	    <version>2.0.10</version>
        </program>
	<program>
            <name>cutadapt</name>
	    <path>/sw/apps/bioinfo/cutadapt/1.2.1/kalkyl/bin/cutadapt</path>
	    <version>1.2.1</version>
        </program>
        <program>
            <name>cufflinks</name>
	    <path>/sw/apps/bioinfo/cufflinks/2.1.1/kalkyl/cufflinks</path>
	    <version>2.1.1</version>
        </program>
        <program>
            <name>cuffdiff</name>
	    <path>/sw/apps/bioinfo/cufflinks/2.1.1/kalkyl/cuffdiff</path>
	    <version>2.1.1</version>
        </program>
        <program>
            <name>fixemptyreads</name>
	    <path>/proj/a2014205/piper_resources/programs/FixEmptyReads.pl</path>
	    <version>1.0</version>
        </program>
        <program>
            <name>snpEff</name>
            <path>/sw/apps/bioinfo/snpEff/4.1/nestor/scripts/snpEff</path>
	    <version>4.1</version>
        </program>
    </programs>
    <resources>
        <resource>
            <name>dbsnp</name>
	    <path>/proj/a2014205/piper_references/gatk_bundle/2.8/b37/dbsnp_138.b37.vcf</path>
	    <version>gatk-bundle/2.8</version>
        </resource>
        <resource>
            <name>indels</name>
	    <path>/proj/a2014205/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>/proj/a2014205/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>/proj/a2014205/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>/proj/a2014205/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>/proj/a2014205/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>/proj/a2014205/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>
          <path>/not/applicable</path>
	  <version>GRCh37.75</version>
        </resource>
    </resources>
</globalConfig>