Notes on setting up and using the google cloud lifesciences pipelines

setup_google_beta_lifesciences.sh

# PROJECT_ID is the billable project code "word-word-number"

#  Having -life-sciences suffix may be important
export BUCKET=gs://PROJECT_ID-life-sciences

# Make a bucket (storage folder) for input and output data
# See intro to installing gsutil in this gist https://gist.github.com/clairemcwhite/ca33c9b7385ee4e2b64641353399f3ba
gsutil mb ${BUCKET}

# First do the example script
# When at first it didn't recognize pipelines, running "$ gcloud components update" fixed it
gcloud beta lifesciences pipelines run \
    --regions us-east1 \
    --command-line 'samtools index ${BAM} ${BAI}' \
    --docker-image "gcr.io/genomics-tools/samtools" \
    --inputs BAM=gs://genomics-public-data/NA12878.chr20.sample.bam \
    --outputs BAI=${BUCKET}/NA12878.chr20.sample.bam.bai
    
# Check status with: Make long number be the job number that was just printed
gcloud beta lifesciences operations wait 012345678987654321

# When it's done see output with
gsutil ls ${BUCKET}

# Now with making own dockerized script, ex. one called "my_docker"

docker build -t my_docker .
docker run my_docker

# Set up to push docker image to the google container registry 
gcloud auth login
gcloud auth configure-docker

# More info on these tag here:https://cloud.google.com/container-registry/docs/pushing-and-pulling
# docker tag localreponame host/projectid/future_reponame_on_google
docker tag my_docker:latest us.gcr.io/PROJECT_ID/my_docker_12345
docker push us.gcr.io/PROJECT-ID/my_docker_12345

# This was prompted at some point
cloud config set project PROJECT-ID

# Add input data to the bucket
gsutil cp testfile.txt $BUCKET

# my_docker
gcloud beta lifesciences pipelines run \
    --regions us-east1 \
    --command-line 'Rscript testscript.R --infile ${IN} --outfile ${OUT}' \
    --docker-image "us.gcr.io/my_docker_12345" \
    --inputs IN=${BUCKET}/testfile.txt\
    --outputs PUT=${BUCKET}/testoutfile.csv

# See if it's done
gcloud beta lifesciences operations wait 13589916798356839505

gsutil ls ${BUCKET}
# get output data back
gsutil cp ${BUCKET}/testoutfile .


## Example of a Dockerfile for R work 

FROM rocker/r-ver:3.6.2
# If using tidyverse functions
#FROM rocker/tidyverse:3.6.1 

# LABEL about the custom image
LABEL maintainer="claire.mcwhite@utexas.edu"
LABEL version="0.1"
LABEL description="This is custom Docker Image for doing an ldproxy_batch query to get proxy snps."

# File Author / Maintainer
MAINTAINER clairemcwhite <claire.mcwhite@utexas.edu>

# Prevents interactive tzdata question
ARG DEBIAN_FRONTEND=noninteractive
ENV TZ=America/New_York

# These were all prompted during attempts to run this docker image
RUN apt-get update && apt-get install --yes --no-install-recommends \
   libcurl4-openssl-dev \
   libssl-dev \
   python3


# Install R packages
RUN install2.r --error \
    LDlinkR \
    argparse

# Script 
ADD batch_ldlinkr.R  /