!(wget ftp://ftp.microbio.me/qiime/tutorial_files/moving_pictures_tutorial-1.9.0.tgz || curl -O ftp://ftp.microbio.me/qiime/tutorial_files/moving_pictures_tutorial-1.9.0.tgz)
!tar -xzf moving_pictures_tutorial-1.9.0.tgz

from IPython.display import FileLinks, FileLink

FileLinks('moving_pictures_tutorial-1.9.0')

FileLink('moving_pictures_tutorial-1.9.0/README.txt')

from functools import partial
from os import chdir

chdir('moving_pictures_tutorial-1.9.0/illumina')
FileLink = partial(FileLink, url_prefix='moving_pictures_tutorial-1.9.0/illumina/')
FileLinks = partial(FileLinks, url_prefix='moving_pictures_tutorial-1.9.0/illumina/')

!validate_mapping_file.py -o vmf-map/ -m map.tsv

!validate_mapping_file.py -o vmf-map-bad/ -m map-bad.tsv 

FileLinks('vmf-map-bad/')

!split_libraries_fastq.py -o slout/ -i forward_reads.fastq.gz -b barcodes.fastq.gz -m map.tsv

FileLinks('slout/')

!count_seqs.py -i slout/seqs.fna

!pick_open_reference_otus.py -o otus/ -i slout/seqs.fna -p ../uc_fast_params.txt

FileLink('otus/index.html')

!biom summarize-table -i otus/otu_table_mc2_w_tax_no_pynast_failures.biom

!core_diversity_analyses.py -o cdout/ -i otus/otu_table_mc2_w_tax_no_pynast_failures.biom -m map.tsv -t otus/rep_set.tre -e 1114

FileLink('cdout/index.html')

!core_diversity_analyses.py -o cdout/ --recover_from_failure -c "SampleType,DaysSinceExperimentStart" -i otus/otu_table_mc2_w_tax_no_pynast_failures.biom -m map.tsv -t otus/rep_set.tre -e 1114

FileLink('cdout/index.html')

!make_emperor.py -i cdout/bdiv_even1114/weighted_unifrac_pc.txt -o cdout/bdiv_even1114/weighted_unifrac_emperor_pcoa_plot -m map.tsv --custom_axes DaysSinceExperimentStart 
!make_emperor.py -i cdout/bdiv_even1114/unweighted_unifrac_pc.txt -o cdout/bdiv_even1114/unweighted_unifrac_emperor_pcoa_plot -m map.tsv --custom_axes DaysSinceExperimentStart 

FileLinks("precomputed-output/")