Nshell Commands

Nshell is a script language to run bash commands inside virtual machines on the cloud. All commands ran by N3phele are written in Nshell. Here is an example:

# createQiimeImage.n
# Based on the following page: https://github.com/qiime/qiime-deploy
name	   : createQiimeImage
description: Create the Qiime image. It will install all required files. After that, you need to create        the image in the console hpcloud at https://console.hpcloud.com/compute/az-1_region-a_geo-1/custom_images
version	   : 1.8.0
preferred  : True
tags	   : qiime
processor  : StackService
public	   : True
icon	   : http://www.n3phele.com/qiimeIcon

HPZone1:
# Creates the createQiimeImageMachine, a standard.xsmall (100) with 1 core. ImageRef = Ubuntu 12.04 64 bits
$$createQiimeImageMachine = CREATEVM  --name createQiimeImageMachine --imageRef 75845 --nodeCount 1 --flavorRef 100

ON $$createQiimeImageMachine
	# Uncomment the universe and multiverse repositories from /etc/apt/sources.list, and add the URL to download the R package
	wget https://region-a.geo-1.objects.hpcloudsvc.com:443/v1/12365734013392/filesToQiime/sources.list 2> /dev/null ;
	sudo mv sources.list /etc/apt/sources.list ;
	sudo apt-get --force-yes -y install python-dev libncurses5-dev libssl-dev libzmq-dev libgsl0-dev openjdk-6-jdk libxml2 libxslt1.1 libxslt1-dev ant git subversion build-essential zlib1g-dev libpng12-dev libfreetype6-dev mpich2 libreadline-dev gfortran unzip libmysqlclient18 libmysqlclient-dev ghc sqlite3 libsqlite3-dev libc6-i386 torque-client libbz2-dev 2> /dev/null ;
	cd ~/sandbox ;
	sudo apt-get install -y git ;
	git clone git://github.com/qiime/qiime-deploy.git ;
	git clone git://github.com/qiime/qiime-deploy-conf.git ;
	cd qiime-deploy/ ;
	sudo apt-get install -y gcc g++ ant openjdk-7-jdk openjdk-7-jre ;
	# Upgrade and update
	sudo apt-get upgrade -y ;
	sudo apt-get update -y ;	
	# Install usearch v5.2.236
	wget http://drive5.com/cgi-bin/upload3.py?license=2014011005224508902 ;
	mv upload3.py\?license\=2014011005224508902 usearch ;
	chmod a+x usearch ;
	sudo mv usearch /bin/ ;
	# Install R package - http://cran-r.c3sl.ufpr.br/index.html
	sudo apt-get install --force-yes -y r-base ;
	# Deploy qiime - The following command will fail, so we have to force it to return true
	python qiime-deploy.py $HOME/sandbox/qiime_software/ -f $HOME/sandbox/qiime-deploy-conf/qiime-1.8.0/qiime.conf --force-remove-failed-dirs || echo qiime-deployed ;
	# Change cloud_environment to true
	cd ~/sandbox ;
	cp qiime_software/qiime_config qiime_software/qiime_config_cloud_environment_false ;
	sed -i -r 's/False/True/' ./qiime_software/qiime_config ;
	# Check installation
	source /home/ubuntu/sandbox/qiime_software/activate.sh ;
	print_qiime_config.py -t || echo printed_qiime_config ;