Uppmax xml config file

uppmax_global_config.xml

@@ -0,0 +1,71 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<globalConfig xmlns="globalconfig.xml.molmed">
+    <programs>
+        <program>
+            <name>bwa</name>
+            <path>/sw/apps/bioinfo/bwa/0.7.5a/milou/bin/bwa</path>
+        </program>
+        <program>
+            <name>samtools</name>
+            <path>/sw/apps/bioinfo/samtools/0.1.19/milou/bin/samtools</path>
+        </program>
+        <program>
+            <name>qualimap</name>
+            <path>/proj/a2009002/piper_resources/programs/qualimap_v1.0/qualimap</path>
+        </program>
+	<program>
+            <name>RNA-SeQC</name>
+            <path>/proj/a2009002/piper_resources/programs/RNA-SeQC_v1.1.7.jar</path>
+        </program>
+	<program>
+            <name>tophat</name>
+            <path>/sw/apps/bioinfo/tophat/2.0.10/kalkyl/bin/tophat2</path>
+        </program>
+	<program>
+            <name>cutadapt</name>
+            <path>/sw/apps/bioinfo/cutadapt/1.2.1/kalkyl/bin/cutadapt</path>
+        </program>
+        <program>
+            <name>cufflinks</name>
+            <path>/sw/apps/bioinfo/cufflinks/2.1.1/kalkyl/cufflinks</path>
+        </program>
+        <program>
+            <name>cuffdiff</name>
+            <path>/sw/apps/bioinfo/cufflinks/2.1.1/kalkyl/cuffdiff</path>
+        </program>
+        <program>
+            <name>fixemptyreads</name>
+            <path>/proj/a2009002/piper_resources/programs/FixEmptyReads.pl</path>
+        </program>
+    </programs>
+    <resources>
+        <resource>
+            <name>dbsnp</name>
+            <path>/proj/a2009002/piper_references/gatk_bundle/2.8/b37/dbsnp_138.b37.vcf</path>
+        </resource>
+        <resource>
+            <name>indels</name>
+            <path>/proj/a2009002/piper_references/gatk_bundle/2.8/b37/Mills_and_1000G_gold_standard.indels.b37.vcf</path>
+        </resource>
+        <resource>
+            <name>indels</name>
+            <path>/proj/a2009002/piper_references/gatk_bundle/2.8/b37/1000G_phase1.indels.b37.vcf</path>
+        </resource>
+        <resource>
+            <name>hapmap</name>
+            <path>/proj/a2009002/piper_references/gatk_bundle/2.8/b37/hapmap_3.3.b37.vcf</path>
+        </resource>
+        <resource>
+            <name>omni</name>
+            <path>/proj/a2009002/piper_references/gatk_bundle/2.8/b37/1000G_omni2.5.b37.vcf</path>
+        </resource>
+        <resource>
+            <name>mills</name>
+            <path>/proj/a2009002/piper_references/gatk_bundle/2.8/b37/Mills_and_1000G_gold_standard.indels.b37.vcf</path>
+        </resource>
+        <resource>
+            <name>thousandGenomes</name>
+            <path>/proj/a2009002/piper_references/gatk_bundle/2.8/b37/1000G_phase1.snps.high_confidence.b37.vcf</path>
+        </resource>
+    </resources>
+</globalConfig>

workflows/WholeGenome.sh

@@ -71,7 +71,7 @@ fi
 #---------------------------------------------
 piper -S ${SCRIPTS_DIR}/DNABestPracticeVariantCalling.scala \
 	      --xml_input ${PIPELINE_SETUP} \
-	      --global_config ../globalConfig.xml \
+	      --global_config uppmax_global_config.xml \
 	      --number_of_threads 8 \
 	      --scatter_gather 23 \
 	      -jobRunner ${JOB_RUNNER} \