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#!/bin/bash
#
#
set -e
set -x
DOWNLOAD_NAME=data_mass_spec_annotated
SCRATCH_DIR=${TMPDIR-/tmp}/mhcflurry-downloads-generation
SCRIPT_ABSOLUTE_PATH="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/$(basename "${BASH_SOURCE[0]}")"
SCRIPT_DIR=$(dirname "$SCRIPT_ABSOLUTE_PATH")
export PYTHONUNBUFFERED=1
mkdir -p "$SCRATCH_DIR"
rm -rf "$SCRATCH_DIR/$DOWNLOAD_NAME"
mkdir "$SCRATCH_DIR/$DOWNLOAD_NAME"
# Send stdout and stderr to a logfile included with the archive.
#exec > >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt")
#exec 2> >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt" >&2)
# Log some environment info
date
pip freeze
git status
cd $SCRATCH_DIR/$DOWNLOAD_NAME
cp $SCRIPT_DIR/annotate.py .
INPUT=$(mhcflurry-downloads path data_curated)/nontraining_curated.by_pmid.csv.bz2
python annotate.py "$INPUT" --out annotated_ms.csv
exit 1
bzip2 annotated_ms.csv
cp $SCRIPT_ABSOLUTE_PATH .
bzip2 LOG.txt
RESULT="$SCRATCH_DIR/${DOWNLOAD_NAME}.$(date +%Y%m%d).tar.bz2"
tar -cjf "$RESULT" *
echo "Created archive: $RESULT"