From 7f48dc7cc944db782baf126722d9628ead453803 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Mon, 19 Feb 2018 21:55:17 -0500
Subject: [PATCH] First cut of models_class1_consensus download
---
.../models_class1_consensus/GENERATE.sh | 49 +++++++++++++++++++
1 file changed, 49 insertions(+)
create mode 100755 downloads-generation/models_class1_consensus/GENERATE.sh
diff --git a/downloads-generation/models_class1_consensus/GENERATE.sh b/downloads-generation/models_class1_consensus/GENERATE.sh
new file mode 100755
index 00000000..e4ded73d
--- /dev/null
+++ b/downloads-generation/models_class1_consensus/GENERATE.sh
@@ -0,0 +1,49 @@
+#!/bin/bash
+#
+# Model select based on consensus (agreement with full ensemble).
+# Uses models trained in models_class1_unselected download.
+#
+set -e
+set -x
+
+DOWNLOAD_NAME=models_class1_consensus
+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
+
+PROCESSORS=$(getconf _NPROCESSORS_ONLN)
+echo "Detected processors: $PROCESSORS"
+
+time mhcflurry-class1-select-allele-specific-models \
+ --models-dir "$(mhcflurry-downloads path models_class1_unselected)/models" \
+ --out-models-dir models \
+ --scoring consensus \
+ --num-jobs $(expr $PROCESSORS \* 2)
+
+time mhcflurry-calibrate-percentile-ranks \
+ --models-dir models \
+ --num-jobs $(expr $PROCESSORS \* 2)
+ --num-peptides-per-length 100000
+
+cp $SCRIPT_ABSOLUTE_PATH .
+bzip2 LOG.txt
+tar -cjf "../${DOWNLOAD_NAME}.tar.bz2" *
+
+echo "Created archive: $SCRATCH_DIR/$DOWNLOAD_NAME.tar.bz2"
--
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