diff --git a/scripts/HUMAnN2_pipeline.sh b/scripts/HUMAnN2_pipeline.sh
new file mode 100755
index 0000000..a729f40
--- /dev/null
+++ b/scripts/HUMAnN2_pipeline.sh
@@ -0,0 +1,52 @@
+#!/usr/bin/env bash
+#$ -o ./log/
+#$ -e ./log/
+
+
+#STEPS
+# run the humann2 
+# renormalize to copies per million and relative abundance 
+# map to KO and EC terms
+# remove the intermediate files
+
+#specify paths 
+
+WORKING_DIR=/klaster/scratch/mmaranga/functional_analysis/diabimmune_data/
+READ_DIR=${WORKING_DIR}/combined_data 
+OUTPUT_DIR=${WORKING_DIR}/uniref90_diabimmune_humman2_analysis 
+MAPPING_FILES=/home/mmaranga/utility_mapping/
+
+cd $WORKING_DIR
+
+# running humann2
+
+for file in $READ_DIR/*fastq.gz
+	do 
+	humann2 -i ${file} -o $OUTPUT_DIR
+done
+
+# Merge gene family and abundance files 
+
+humann2_join_tables -i $OUTPUT_DIR -o $OUTPUT_DIR/merged_genefamilies.tsv --file_name genefamilies
+
+humann2_join_tables -i $OUTPUT_DIR -o $OUTPUT_DIR/merged_pathabundance.tsv --file_name pathabundance
+
+humann2_join_tables -i $OUTPUT_DIR -o $OUTPUT_DIR/merged_pathcoverage.tsv --file_name pathcoverage
+
+# normalization
+#normalizing to copies per million
+humann2_renorm_table -i $OUTPUT_DIR/merged_genefamilies.tsv -o $OUTPUT_DIR/normalized_genefamilies_cpm.tsv --units cpm
+humann2_renorm_table -i $OUTPUT_DIR/merged_pathabundance.tsv -o $OUTPUT_DIR/normalized_pathabundance_cpm.tsv --units cpm
+
+# normalizing to relative abundance
+humann2_renorm_table -i $OUTPUT_DIR/merged_genefamilies.tsv -o  $OUTPUT_DIR/normalized_genefamilies_relab.tsv --units relab
+humann2_renorm_table -i $OUTPUT_DIR/merged_pathabundance.tsv -o $OUTPUT_DIR/normalized_pathabundance_relab.tsv --units relab
+
+# map to KO  
+humann2_regroup_table -i $OUTPUT_DIR/normalized_genefamilies_cpm.tsv -o $OUTPUT_DIR/normalized_genefamilies_cpm_KO.tsv -c $MAPPING_FILES/map_ko_uniref90.txt.gz 
+
+# map genefamilies abundance to Enzyme Commission (EC) terms
+humann2_regroup_table -i $OUTPUT_DIR/normalized_genefamilies_cpm.tsv -o $OUTPUT_DIR/normalized_genefamilies_cpm_EC.tsv -c $MAPPING_FILES/map_level4ec_uniref90.txt.gz
+
+# remove the intermediate files
+rm -rf $OUTPUT_DIR/*_humann2_temp