marcusrussi · May 27, 2021 22:15
diff --git a/harvard-cluster-nextflow-covidestim-install.sh b/harvard-cluster-nextflow-covidestim-install.sh
 cd ~

 # Get an interactive session. --mem is important otherwise
 # you will probably get "OOM-killed" later on
 srun --pty -p test --mem=4G --time=120 bash

 # Load Java and Conda
 module load jdk/1.8.0_172-fasrc01 # This MIGHT not be neccessary, but doesn't hurt..
 module load Anaconda3/2019.10

 # Add the Bioconda "channels" (~= repositories) to your Conda
 # setup. Nextflow is available in Bioconda.
 conda config --add channels bioconda
 conda config --add channels conda-forge

 # Install Nextflow into a Conda environment named "covidestim"
 conda create -n covidestim nextflow awscli

 # After agreeing to the proposed list of packages to install, wait
 # like 10-20 minutes for all the deps to install

 # ...

 # Initialize your shell to work with Conda
 conda init bash

 # IMPORTANT: close and re-open your shell. Hit Ctrl-D, then:
 srun --pty -p test --mem=4G bash

 # Activate the "covidestim" Conda environment
 conda activate covidestim

 # Verify Nextflow works
 nextflow run hello

 # After a few seconds, you should get the following output:
 # N E X T F L O W  ~  version 21.04.0
 # Pulling nextflow-io/hello ...
 #  downloaded from https://github.com/nextflow-io/hello.git
 # Launching `nextflow-io/hello` [big_khorana] - revision: e6d9427e5b [master]
 # executor >  local (4)
 # [cd/ea5bd4] process > sayHello (3) [100%] 4 of 4 ✔
 # Ciao world!
 #
 # Bonjour world!
 # 
 # Hola world!
 # 
 # Hello world!

 ############################################
 ## Performing an example covidestim run   ##
 ############################################

 # Use Ctrl-D to get back to a login node (right now you are
 # probably on the interactive partition, which might cause
 # job submission issues)

 # cd to the high-speed filesystem (/n/holyscratch01)
 cd /n/holyscratch01/menzies_lab/Everyone

 # make a unique directory to store the run's files
 mkdir mwr_covidestim_test01 && cd mwr_covidestim_test01

 # Paste the following into a file `runscript.sh` using Vim/etc:
 #!/usr/bin/bash

 module load Anaconda3/2019.10
 conda activate covidestim

 # -Run the `master` branch of `dailyFlow`
 # -Don't publish to AWS S3
 # -Run the HEAD commit of the `master` branch
 # -27 processes for the 52 states (+DC,PR)
 # -Never use the sampler
 # -Run using Slurm and Singularity
 # -Use the `master` branch of `covidestim`
 # -Run states
 # -Results to `results/`
 # -Today's date
 nextflow run covidestim/dailyFlow \
  -r "master" \
  --s3pub false \
  -latest \
  --ngroups 27 \
  --alwaysoptimize \
  -profile "slurm,states" \
  --branch master \
  --key state \
  --outdir results \
  --date "$(date '+%Y-%m-%d')"
  
 #### END FILE! ####

 # Run the script for a few hours on the shared partition
 sbatch -p shared --time=240 --mem=8G runscript.sh

 # Results will eventually be in the `results/` folder
	cd ~

	# Get an interactive session. --mem is important otherwise
	# you will probably get "OOM-killed" later on
	srun --pty -p test --mem=4G --time=120 bash

	# Load Java and Conda
	module load jdk/1.8.0_172-fasrc01 # This MIGHT not be neccessary, but doesn't hurt..
	module load Anaconda3/2019.10

	# Add the Bioconda "channels" (~= repositories) to your Conda
	# setup. Nextflow is available in Bioconda.
	conda config --add channels bioconda
	conda config --add channels conda-forge

	# Install Nextflow into a Conda environment named "covidestim"
	conda create -n covidestim nextflow awscli

	# After agreeing to the proposed list of packages to install, wait
	# like 10-20 minutes for all the deps to install

	# ...

	# Initialize your shell to work with Conda
	conda init bash

	# IMPORTANT: close and re-open your shell. Hit Ctrl-D, then:
	srun --pty -p test --mem=4G bash

	# Activate the "covidestim" Conda environment
	conda activate covidestim

	# Verify Nextflow works
	nextflow run hello

	# After a few seconds, you should get the following output:
	# N E X T F L O W ~ version 21.04.0
	# Pulling nextflow-io/hello ...
	# downloaded from https://github.com/nextflow-io/hello.git
	# Launching `nextflow-io/hello` [big_khorana] - revision: e6d9427e5b [master]
	# executor > local (4)
	# [cd/ea5bd4] process > sayHello (3) [100%] 4 of 4 ✔
	# Ciao world!
	#
	# Bonjour world!
	#
	# Hola world!
	#
	# Hello world!

	############################################
	## Performing an example covidestim run ##
	############################################

	# Use Ctrl-D to get back to a login node (right now you are
	# probably on the interactive partition, which might cause
	# job submission issues)

	# cd to the high-speed filesystem (/n/holyscratch01)
	cd /n/holyscratch01/menzies_lab/Everyone

	# make a unique directory to store the run's files
	mkdir mwr_covidestim_test01 && cd mwr_covidestim_test01

	# Paste the following into a file `runscript.sh` using Vim/etc:
	#!/usr/bin/bash

	module load Anaconda3/2019.10
	conda activate covidestim

	# -Run the `master` branch of `dailyFlow`
	# -Don't publish to AWS S3
	# -Run the HEAD commit of the `master` branch
	# -27 processes for the 52 states (+DC,PR)
	# -Never use the sampler
	# -Run using Slurm and Singularity
	# -Use the `master` branch of `covidestim`
	# -Run states
	# -Results to `results/`
	# -Today's date
	nextflow run covidestim/dailyFlow \
	-r "master" \
	--s3pub false \
	-latest \
	--ngroups 27 \
	--alwaysoptimize \
	-profile "slurm,states" \
	--branch master \
	--key state \
	--outdir results \
	--date "$(date '+%Y-%m-%d')"

	#### END FILE! ####

	# Run the script for a few hours on the shared partition
	sbatch -p shared --time=240 --mem=8G runscript.sh

	# Results will eventually be in the `results/` folder
No results found