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fix: Fix download script variable names #61

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Mar 28, 2024
Merged

fix: Fix download script variable names #61

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34 changes: 17 additions & 17 deletions download-data.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ export STATIC_INFIX=${STATIC_INFIX-varfish-static}
# Overall directory prefix.
export DIR_PREFIX=${DIR_PREFIX-.dev}
# Overall static data directory.
export DATA_DIR=${DATA_DIR-$DIR_PREFIX/volumes/$STATIC_DIR/data}
export DATA_DIR=${DATA_DIR-$DIR_PREFIX/volumes/$STATIC_INFIX/data}
# S3 endpoing URL.
export S3_ENDPOINT_URL=https://ceph-s3-public.cubi.bihealth.org
# Grep regex expression for downloading data.
Expand All @@ -43,7 +43,7 @@ fi
# annonars
export V_ANNONARS=${V_ANNONARS-0.33.0}
# annonars for annonars/genes
export V_ANNONARS_ANNONARS_GENES=${V_ANNONARS_ANNONARS_GENES-0.34.0}
export V_ANNONARS_GENES=${V_ANNONARS_GENES-0.34.0}
# viguno
export V_VIGUNO=${V_VIGUNO-0.2.0}
# VarFish Worker
Expand Down Expand Up @@ -234,7 +234,7 @@ annonars/dbsnp-grch37-$V_DBSNP+$V_ANNONARS
annonars/dbsnp-grch38-$V_DBSNP+$V_ANNONARS
annonars/functional-grch37-$V_REFSEQ_GRCH37+$V_ANNONARS
annonars/functional-grch38-$V_REFSEQ_GRCH38+$V_ANNONARS
annonars/genes-$V_ACMG_SF+$V_GNOMAD_CONSTRAINTS+$V_DBNSFP_NO_SUFFIX+$V_HPO_ANNONARS_GENES+$V_VARFISHDB_ANNONARS_GENES+$V_ANNONARS_ANNONARS_GENES
annonars/genes-$V_ACMG_SF+$V_GNOMAD_CONSTRAINTS+$V_DBNSFP_NO_SUFFIX+$V_HPO+$V_ORPHAPACKETS+$V_VARFISHDB+$V_ANNONARS
annonars/gnomad-exomes-grch37-$V_GNOMAD_EXOMES_GRCH37+$V_ANNONARS
annonars/gnomad-exomes-grch38-$V_GNOMAD_EXOMES_GRCH38+$V_ANNONARS
annonars/gnomad-genomes-grch37-$V_GNOMAD_EXOMES_GRCH37+$V_ANNONARS
Expand Down Expand Up @@ -293,7 +293,7 @@ EOF

rm -f $DATA_DIR/annonars/genes
ln -sr \
$DATA_DIR/download/annonars/genes-$V_ACMG_SF+$V_GNOMAD_CONSTRAINTS+$V_DBNSFP_NO_SUFFIX+$V_HPO_ANNONARS_GENES+$V_VARFISHDB_ANNONARS_GENES+$V_ANNONARS_ANNONARS_GENES \
$DATA_DIR/download/annonars/genes-$V_ACMG_SF+$V_GNOMAD_CONSTRAINTS+$V_DBNSFP_NO_SUFFIX+$V_HPO+$V_ORPHAPACKETS+$V_VARFISHDB+$V_ANNONARS \
$DATA_DIR/annonars/genes

# cadd - GRCh37
Expand Down Expand Up @@ -595,8 +595,8 @@ if [[ "$STEPS" = *other* ]]; then

log_info "- dotty"

mkdir -p $DIR_PREFIX/volumes/$STATIC_DIR/data/download/dotty
pushd $DIR_PREFIX/volumes/$STATIC_DIR/data/download/dotty >/dev/null
mkdir -p $DIR_PREFIX/volumes/$STATIC_INFIX/data/download/dotty
pushd $DIR_PREFIX/volumes/$STATIC_INFIX/data/download/dotty >/dev/null
wget -q -c \
https://github.com/SACGF/cdot/releases/download/v$V_DOTTY_CDOT_VERSION/cdot-$V_DOTTY_CDOT_VERSION.ensembl.grch37.json.gz \
https://github.com/SACGF/cdot/releases/download/v$V_DOTTY_CDOT_VERSION/cdot-$V_DOTTY_CDOT_VERSION.ensembl.grch38.json.gz \
Expand All @@ -608,26 +608,26 @@ if [[ "$STEPS" = *other* ]]; then
cat seqrepo.tar.gz-?? | tar -xzf -
popd >/dev/null

mkdir -p $DIR_PREFIX/volumes/$STATIC_DIR/data/dotty
rm -f $DIR_PREFIX/volumes/$STATIC_DIR/data/dotty/{*.json.gz,seqrepo}
ln -sr $DIR_PREFIX/volumes/$STATIC_DIR/data/download/dotty/{*.json.gz,seqrepo} \
$DIR_PREFIX/volumes/$STATIC_DIR/data/dotty
mkdir -p $DIR_PREFIX/volumes/$STATIC_INFIX/data/dotty
rm -f $DIR_PREFIX/volumes/$STATIC_INFIX/data/dotty/{*.json.gz,seqrepo}
ln -sr $DIR_PREFIX/volumes/$STATIC_INFIX/data/download/dotty/{*.json.gz,seqrepo} \
$DIR_PREFIX/volumes/$STATIC_INFIX/data/dotty

log_info "- cada-prio"

mkdir -p $DIR_PREFIX/volumes/$STATIC_DIR/data/download/cada
pushd $DIR_PREFIX/volumes/$STATIC_DIR/data/download/cada >/dev/null
mkdir -p $DIR_PREFIX/volumes/$STATIC_INFIX/data/download/cada
pushd $DIR_PREFIX/volumes/$STATIC_INFIX/data/download/cada >/dev/null
wget -q -c \
https://github.com/bihealth/cada-prio-data/releases/download/cada-prio-data-$V_CADA_PRIO_MODEL/cada-prio-model-$V_CADA_PRIO_MODEL+$V_CADA_PRIO_VERSION.tar.gz
tar -xzf cada-prio-model-$V_CADA_PRIO_MODEL+$V_CADA_PRIO_VERSION.tar.gz
popd >/dev/null

mkdir -p $DIR_PREFIX/volumes/$STATIC_DIR/data/cada
rm -f $DIR_PREFIX/volumes/$STATIC_DIR/data/cada/model
mkdir -p $DIR_PREFIX/volumes/$STATIC_INFIX/data/cada
rm -f $DIR_PREFIX/volumes/$STATIC_INFIX/data/cada/model

source_dir="$DIR_PREFIX/volumes/$STATIC_DIR/data/download/cada/cada-prio-model-$V_CADA_PRIO_MODEL+$V_CADA_PRIO_VERSION/model"
source_dir="$DIR_PREFIX/volumes/$STATIC_INFIX/data/download/cada/cada-prio-model-$V_CADA_PRIO_MODEL+$V_CADA_PRIO_VERSION/model"
for file in "${source_dir}"/*; do
rm -f "$DIR_PREFIX/volumes/$STATIC_DIR/data/cada/$(basename "$file")"
ln -sr "$file" "$DIR_PREFIX/volumes/$STATIC_DIR/data/cada/"
rm -f "$DIR_PREFIX/volumes/$STATIC_INFIX/data/cada/$(basename "$file")"
ln -sr "$file" "$DIR_PREFIX/volumes/$STATIC_INFIX/data/cada/"
done
fi
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