metaphlan2

wget https://bitbucket.org/biobakery/metaphlan2/get/default.zip
unzip default.zip
mv biobakery-metaphlan2-0c3ed7b7718b metaphlan2
cd metaphlan2/
export PATH=`pwd`:`pwd`/utils:$PATH
export mpa_dir=`pwd`
metaphlan2.py 
metaphlan2.py SCN_tr_cor_1.fastq,SCN_tr_cor_2.fastq --bowtie2out SCN.bowtie2.bz2 --nproc 8 --input_type fastq > profiled_SCN.txt