runGeneratorForQIIMETutorial.n

# runGeneratorForQIIMETutorial.n
name       : runGeneratorForQIIMETutorial
description: Use generator to create nshell scripts for QIIME scripts
version    : 1.8.0
preferred  : True
tags       : qiime service
processor  : StackService
public     : True
icon       : http://www.n3phele.com/qiimeIcon
input files:
	input_fp.file # file to concatenate in generator
output files:
  nshells.zip # generated nshell scripts
HPZone1:
  ON $$createQiimeImageMachine --produces [nshells.zip: nshells.zip]
    cd ~ ;
    sudo mkdir ~/generator_output ;
    sudo chmod 077 ~/generator_output ;
    git clone git://github.com/n3phele/nshell-generator.git ;

    # Need to move generator because it needs to be in the same folder as the scripts
    mv nshell-generator/scripts/make_nshell.py sandbox/qiime_software/qiime-1.8.0-release/scripts ;
    mv nshell-generator/scripts/nshell_generator.py sandbox/qiime_software/qiime-1.8.0-release/scripts ;
    cd sandbox/qiime_software/qiime-1.8.0-release/scripts ;

    # Execute this to fix python path
    source /home/ubuntu/sandbox/qiime_software/activate.sh ;

	mv ~/sandbox/input_fp.file ~/sandbox/qiime_software/qiime-1.8.0-release/scripts ;
	
    python make_nshell.py -o ~/generator_output -s validate_mapping_file.py -z HPZone1 -m generatorVM -i 373455 ;
    python make_nshell.py -o ~/generator_output -s split_libraries.py -z HPZone1 -m generatorVM -i 373455 ;

    # This script needs more memory to run properly
    # This could also cause an error because of the Greengenes dependency that is not installed properly by QIIME
    python make_nshell.py -o ~/generator_output -s pick_de_novo_otus.py -z HPZone1 -m generatorVM -f 104 -i 373455 -c input_fp.file ;
    python make_nshell.py -o ~/generator_output -s make_otu_network.py -z HPZone1 -m generatorVM -i 373455 ;
    python make_nshell.py -o ~/generator_output -s summarize_taxa_through_plots.py -z HPZone1 -m generatorVM -i 373455 ;

    cd ~/generator_output ;
    zip -r nshells ./ ;
    mv nshells.zip ~/sandbox ;