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chore: bump mehari tx version #70

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merged 1 commit into from
Nov 22, 2024
Merged

chore: bump mehari tx version #70

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18 changes: 10 additions & 8 deletions download-data.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -108,7 +108,7 @@ export V_CLINGEN_REGIONS=${V_CLINGEN_REGIONS-20240105}
# Mehari Gene ID Xlink
export V_MEHARI_XLINK=${V_MEHARI_XLINK-20240105}
# Mehari Transcripts
export V_MEHARI_TXS=${V_MEHARI_TXS-0.6.0}
export V_MEHARI_TXS=${V_MEHARI_TXS-0.8.1}

# dbVar version
export V_DBVAR=${V_DBVAR-20231030}
Expand Down Expand Up @@ -544,16 +544,18 @@ if [[ "$STEPS" = *other* ]]; then
mkdir -p $DATA_DIR/download/mehari-data-txs-grch3{7,8}

for ext in .zst .zst.sha256 .zst.report .zst.report.sha256; do
for release in grch37 grch38; do
wget -q -c -O $DATA_DIR/download/mehari-data-txs-$release/mehari-data-txs-$release-$V_MEHARI_TXS.bin$ext \
https://github.com/bihealth/mehari-data-tx/releases/download/v$V_MEHARI_TXS/mehari-data-txs-$release-$V_MEHARI_TXS.bin$ext
for release in GRCh37 GRCh38; do
release_lower=$(echo $release | tr '[:upper:]' '[:lower:]')
wget -q -c -O $DATA_DIR/download/mehari-data-txs-$release_lower/mehari-data-txs-$release-refseq-$V_MEHARI_TXS.bin$ext \
https://github.com/bihealth/mehari-data-tx/releases/download/v$V_MEHARI_TXS/mehari-data-txs-$release-refseq-$V_MEHARI_TXS.bin$ext
done
done

for release in grch37 grch38; do
rm -f $DATA_DIR/mehari/$release/txs.bin.zst
ln -sr $DATA_DIR/download/mehari-data-txs-$release/mehari-data-txs-$release-$V_MEHARI_TXS.bin.zst \
$DATA_DIR/mehari/$release/txs.bin.zst
for release in GRCh37 GRCh38; do
release_lower=$(echo $release | tr '[:upper:]' '[:lower:]')
rm -f $DATA_DIR/mehari/$release_lower/txs.bin.zst
ln -sr $DATA_DIR/download/mehari-data-txs-$release/mehari-data-txs-$release-refseq-$V_MEHARI_TXS.bin.zst \
$DATA_DIR/mehari/$release_lower/txs.bin.zst
done

log_info "- clinvar"
Expand Down