run_msconvert_parallel.sh

#!/bin/bash

# Licensed to the Apache Software Foundation (ASF) under one
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# to you under the Apache License, Version 2.0 (the
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#   http://www.apache.org/licenses/LICENSE-2.0

# Unless required by applicable law or agreed to in writing,
# software distributed under the License is distributed on an
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# specific language governing permissions and limitations
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# Author: Fengchao Yu

set -x

threads=16

find ./ -name '*.raw' | parallel -j $threads '
  f2={/.}.mzML
  log_file={/.}.log
  if [ ! -f $f2 ];
  then
    outdir=$(dirname {})
    wine msconvert --64 --zlib --filter "peakPicking" --filter "zeroSamples removeExtra 1-" --outdir $outdir {} >$log_file 2>&1
  fi
'