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#!/bin/bash
#
# Train standard MHCflurry Class I models.
# Calls mhcflurry-class1-train-allele-specific-models on curated training data
# using the hyperparameters in "hyperparameters.yaml".
#
set -e
set -x
DOWNLOAD_NAME=models_class1
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")
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
mkdir models
cp $SCRIPT_DIR/hyperparameters.yaml .
time mhcflurry-class1-train-allele-specific-models \
--data "$(mhcflurry-downloads path data_curated)/curated_training_data.with_mass_spec.csv.bz2" \
--hyperparameters hyperparameters.yaml \
--out-models-dir models \
--percent-rank-calibration-num-peptides-per-length 1000000 \
--min-measurements-per-allele 75 \
cp $SCRIPT_ABSOLUTE_PATH .
bzip2 LOG.txt
tar -cjf "../${DOWNLOAD_NAME}.tar.bz2" *
echo "Created archive: $SCRATCH_DIR/$DOWNLOAD_NAME.tar.bz2"