!(wget ftp://ftp.microbio.me/qiime/tutorial_files/its-soils-tutorial.tgz || curl -O ftp://ftp.microbio.me/qiime/tutorial_files/its-soils-tutorial.tgz)
!(wget ftp://ftp.microbio.me/qiime/tutorial_files/its_12_11_otus.tgz ||  curl -O ftp://ftp.microbio.me/qiime/tutorial_files/its_12_11_otus.tgz)

!tar -xzf its-soils-tutorial.tgz
!tar -xzf its_12_11_otus.tgz
!gunzip ./its_12_11_otus/rep_set/97_otus.fasta.gz
!gunzip ./its_12_11_otus/taxonomy/97_otu_taxonomy.txt.gz

from IPython.display import FileLink, FileLinks
FileLinks('its-soils-tutorial')

!cat its-soils-tutorial/params.txt

!pick_open_reference_otus.py -i its-soils-tutorial/seqs.fna -r its_12_11_otus/rep_set/97_otus.fasta -o otus/ -p its-soils-tutorial/params.txt --suppress_align_and_tree

FileLink('otus/index.html')

!biom summarize-table -i otus/otu_table_mc2_w_tax.biom

!core_diversity_analyses.py -i otus/otu_table_mc2_w_tax.biom -o cdout/ -m its-soils-tutorial/map.txt -e 353 --nonphylogenetic_diversity

FileLink('cdout/index.html')

FileLinks("its-soils-tutorial/precomputed-output/")