From c515aee9111b00fa6284c2610544d8533d5984ac Mon Sep 17 00:00:00 2001
From: Timothy ODonnell <odonnt02@li03c03.chimera.hpc.mssm.edu>
Date: Fri, 3 Jan 2020 08:34:30 -0500
Subject: [PATCH] fix
---
.../models_class1_pan_variants/GENERATE.sh | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/downloads-generation/models_class1_pan_variants/GENERATE.sh b/downloads-generation/models_class1_pan_variants/GENERATE.sh
index 3302dab7..585fd819 100755
--- a/downloads-generation/models_class1_pan_variants/GENERATE.sh
+++ b/downloads-generation/models_class1_pan_variants/GENERATE.sh
@@ -89,14 +89,17 @@ do
if [ "$kind" == "no_additional_ms" ]
then
TRAINING_DATA="$(mhcflurry-downloads path data_curated)/curated_training_data.no_additional_ms.csv.bz2"
+ HYPERPARAMETERS=hyperparameters.production.yaml
fi
if [ "$kind" == "ms_only" ]
then
TRAINING_DATA="$(mhcflurry-downloads path data_curated)/curated_training_data.mass_spec.csv.bz2"
+ HYPERPARAMETERS=hyperparameters.production.yaml
fi
if [ "$kind" == "affinity_only" ]
then
TRAINING_DATA="$(mhcflurry-downloads path data_curated)/curated_training_data.affinity.csv.bz2"
+ HYPERPARAMETERS=hyperparameters.production.yaml
fi
mhcflurry-class1-train-pan-allele-models \
@@ -123,7 +126,7 @@ do
--min-models 2 \
--max-models 8 \
$PARALLELISM_ARGS
- ln -s "$MODELS_DIR/train_data.csv.bz2" "models.${kind}/train_data.csv.bz2"
+ cp "$MODELS_DIR/train_data.csv.bz2" "models.${kind}/train_data.csv.bz2"
done
cp $SCRIPT_ABSOLUTE_PATH .
@@ -153,4 +156,4 @@ mv models.unselected.* .ignored/
RESULT="$SCRATCH_DIR/${DOWNLOAD_NAME}.selected.$(date +%Y%m%d).tar.bz2"
tar -cjf "$RESULT" *
mv .ignored/* . && rmdir .ignored
-echo "Created archive: $RESULT"
\ No newline at end of file
+echo "Created archive: $RESULT"
--
GitLab