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@zachcp
Last active February 9, 2018 14:09
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Antismash 4.0.1 Docker Error with Clusterblast
# Download NRPS/PKS CLusters
AS4 = run_AS_4.sh
# Abysomycin as Example PKS BGC1
PKS.gb:
wget -O $@ http://mibig.secondarymetabolites.org/repository/BGC0000001/BGC0000001.1.final.gbk
PKS_AS4/PKS/BGC0000001.1.final.gbk: PKS.gb
bash $(AS4) PKS.gb PKS_AS4 --clusterblast --knownclusterblast --subclusterblast --smcogs --verbose
all: PKS_AS4/PKS/BGC0000001.1.final.gbk
#!/bin/bash
set -o errexit
set -o nounset
function realpath() {
echo $(readlink -f $1 2>/dev/null || python -c "import sys; import os; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" $1)
}
# handle input file
readonly INPUT_FILE=$(basename $1)
readonly INPUT_DIR=$(dirname $(realpath $1))
shift
# handle output file
readonly OUTPUT_DIR=$(realpath $1)
shift
# Links within the container
readonly CONTAINER_SRC_DIR=/input
readonly CONTAINER_DST_DIR=/output
if [ ! -d ${OUTPUT_DIR} ]; then
mkdir ${OUTPUT_DIR}
fi
# ideally, the input directory would be mounted read only, but currently
# antiSMASH doesn't support parsing from a read only file
docker run \
--volume ${INPUT_DIR}:${CONTAINER_SRC_DIR}:ro \
--volume ${OUTPUT_DIR}:${CONTAINER_DST_DIR}:rw \
--detach=false \
--rm \
--user=$(id -u):$(id -g) \
antismash/standalone:4.0.1 \
${INPUT_FILE} \
$@
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