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auto-asm.sh.sample
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auto-asm.sh.sample
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#!/bin/bash
set -euo pipefail
# Output directory
WORKDIR=`pwd`
# Path to snakemake config file
CONFIG="${WORKDIR}/config.yaml"
# Path to snakemake cluster configuration file
CLUSTER_CONFIG="cluster.json"
# Path to write the final HTML snakemake report
REPORT="${WORKDIR}/auto-asm.html"
# snakemake cluster job submission code
CLUSTER='qsub'
CLUSTER+=' -cwd'
CLUSTER+=' -terse'
CLUSTER+=' -pe parallel {cluster.cores}'
CLUSTER+=' -N {cluster.jobname}'
CLUSTER+=' -l h_vmem={cluster.mem_mb}M'
CLUSTER+=' -l mem_free={cluster.mem_mb}M'
CLUSTER+=' -l h_rt={cluster.walltime}'
CLUSTER+=' -o '$WORKDIR'/{cluster.error}'
CLUSTER+=' -e '$WORKDIR'/{cluster.output}'
CLUSTER+=' {cluster.other_options}'
# Maximum number of concurrent snakemake jobs (local + cluster)
MAX_JOBS=12
# Number of cores on submit node, on which local rules are executed
LOCAL_CORES=4
# Resource limits for auto-asm
RESOURCES='cores=128'
RESOURCES+=' mem_mb=1000000'
# Number of seconds to wait for output files upon rule completion
LATENCY_WAIT=60
# Run snakemake
if snakemake \
--use-conda \
--timestamp \
--configfile $CONFIG \
--cluster-config $CLUSTER_CONFIG \
--cluster "$CLUSTER" \
--jobs $MAX_JOBS \
--local-cores $LOCAL_CORES \
--resources $RESOURCES \
--directory $WORKDIR \
--latency-wait $LATENCY_WAIT \
$*
then
# Generate the report if snakemake finished without error
snakemake \
--timestamp \
--configfile $CONFIG \
--directory $WORKDIR \
--report $REPORT \
$*
fi