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|
#!/bin/bash
#source /localdisk/home/s1680070/.bashrc
#conda activate pangolin
TODAY=$(date +%F)
OUT=${TODAY}_pangoLEARN
OUTDIR=/localdisk/home/shared/raccoon-dog/$OUT
echo $OUTDIR
if [ -d $OUTDIR ]
then
echo "Directory $OUTDIR exists."
els
mkdir $OUTDIR
echo "Directory $OUTDIR does not exist, making it."
fi
echo "Training model version: $TODAY"
if [ -z "$1" ]
then
UID="s1680070"
else
UID=$1
fi
if [ -z "$2" ]
then
DATA_DATE=$TODAY
else
DATA_DATE=$2
fi
echo "training version $DATA_DATE"
# LATEST_DATA=$(ls -td /localdisk/home/shared/raccoon-dog/2021*_gisaid/publish/gisaid | head -n 1)
REPO_PATH=/localdisk/home/s1680070/repositories
PANGO_PATH=$REPO_PATH/pango-designation
PLEARN_PATH=$REPO_PATH/pangoLEARN
echo "pango designation path $PANGO_PATH"
echo "pangoLEARN path $PLEARN_PATH"
cd $PANGO_PATH && git pull #gets any updates to the reports in the data directory
PANGO_VERSION=$(git describe --tags --abbrev=0)
echo $PANGO_VERSION
cd /localdisk/home/shared/raccoon-dog/ #gets any updates to the reports in the data directory
echo "--config outdir=$OUTDIR data_date=$DATA_DATE pangolearn_version=$TODAY "
echo "pangoLEARN training starting" | mail -s "update lineageTree.pb with pango designation version $PANGO_VERSION" angie@soe.ucsc.edu
snakemake --snakefile $PLEARN_PATH/pangoLEARN/scripts/curate_alignment.smk --rerun-incomplete --nolock --cores 1 --config repo_path=$REPO_PATH outdir=$OUTDIR data_date=$DATA_DATE pangolearn_version=$TODAY pango_version=$PANGO_VERSION
|
