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map.sh
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map.sh
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#!/bin/bash -x
# Bismark-ENCODE-WGBS 0.0.1
# Generated by dx-app-wizard.
#
# Basic execution pattern: Your app will run on a single machine from
# beginning to end.
#
# Your job's input variables (if any) will be loaded as environment
# variables before this script runs. Any array inputs will be loaded
# as bash arrays.
#
# Any code outside of main() (or any entry point you may add) is
# ALWAYS executed, followed by running the entry point itself.
#
# See https://wiki.dnanexus.com/Developer-Portal for tutorials on how
# to modify this file.
set -x
set +e
main() {
echo "getting files"
dx download "$genome" -o - | gunzip > genome.fa
dx download "$meIndex" -o - | tar zxvf -
read_fn=`dx describe "$trimmed_reads" --name | cut -d'.' -f1`
dx download "$trimmed_reads" -o - | gunzip > "$read_fn".fq
mv genome.fa input
echo `ls input`
mkdir output
bismark -n 1 -l 28 -output_dir output --temp_dir output input "$read_fn".fq
# Fill in your application code here.
#
# To report any recognized errors in the correct format in
# $HOME/job_error.json and exit this script, you can use the
# dx-jobutil-report-error utility as follows:
#
# dx-jobutil-report-error "My error message"
#
# Note however that this entire bash script is executed with -e
# when running in the cloud, so any line which returns a nonzero
# exit code will prematurely exit the script; if no error was
# reported in the job_error.json file, then the failure reason
# will be AppInternalError with a generic error message.
# The following line(s) use the dx command-line tool to upload your file
# outputs after you have created them on the local file system. It assumes
# that you have used the output field name for the filename for each output,
# but you can change that behavior to suit your needs. Run "dx upload -h"
# to see more options to set metadata.
echo `ls /home/dnanexus/output`
outfile="$read_fn".mapped_methylseq.tgz
tar zcvf $outfile output
mapped_files=$(dx upload /home/dnanexus/$outfile --brief)
# The following line(s) use the utility dx-jobutil-add-output to format and
# add output variables to your job's output as appropriate for the output
# class. Run "dx-jobutil-add-output -h" for more information on what it
# does.
dx-jobutil-add-output mapped_files "$mapped_files" --class=file
}