run-gcp

#!/usr/bin/env bash
#$ -t 1
#$ -V
#$ -j y
#$ -cwd
#$ -o /dev/null
#$ -e /dev/null

# An example bash script demonstrating how to run the entire snakemake pipeline
# This script creates two separate log files:
# 	1) log - the basic snakemake log of completed rules
# 	2) qlog - a more detailed log of the progress of each rule and any errors

# Before running this snakemake pipeline, remember to verify that the config
# file has been appropriately completed with the required input info. In
# particular, make sure that you have created a samples.tsv file specifying
# paths to the fastq files for each of your samples.
# Make sure that this script is executed from the directory that it lives in!

mkdir -p log

# clear leftover log files
if [ -f "log/log" ]; then
	echo ""> "log/log";
fi
if [ -f "log/qlog" ]; then
	echo ""> "log/qlog";
fi

# try to find and activate the snakemake conda env if we need it
if ! command -v 'snakemake' &>/dev/null && \
   command -v 'conda' &>/dev/null && \
   [ "$CONDA_DEFAULT_ENV" != "snakemake" ] && \
   conda info --envs | grep "$CONDA_ROOT/snakemake" &>/dev/null; then
	echo "Snakemake not detected. Attempting to switch to snakemake environment." >> "log/log"
	eval "$(conda shell.bash hook)"
	conda activate snakemake
fi

# you should change the google life sciences values to whatever works for your setup!
# see https://snakemake.readthedocs.io/en/stable/executor_tutorial/google_lifesciences.html
snakemake \
--google-lifesciences \
--default-remote-prefix salk-mcvicker-poc_test \
--google-lifesciences-region us-west2 \
--default-resources 'disk_mb=35000' \
-j \
--notemp \
--latency-wait 120 \
--use-conda \
"$@" &>"log/log"

# message the user on slack if possible
exit_code="$?"
if command -v 'slack' &>/dev/null; then
	if [ "$exit_code" -eq 0 ]; then
		slack "snakemake finished successfully" &>/dev/null
	else
		slack "$(tail -n4 "log/log")" &>/dev/null
	fi
fi
exit "$exit_code"