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docs: updating ClinVar download instructions (#31)
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holtgrewe authored Nov 2, 2023
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Showing 1 changed file with 17 additions and 14 deletions.
31 changes: 17 additions & 14 deletions README.md
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Expand Up @@ -265,27 +265,30 @@ varfish-server-worker db to-bin \
To obtain ClinVar
```bash session
wget -O /tmp/annonars-clinvar-minimal-grch37-20230910+0.18.0.tar.gz \
https://github.com/bihealth/annonars-data-clinvar/releases/download/clinvar-weekly-20230910/annonars-clinvar-minimal-grch37-20230910+0.18.0.tar.gz
wget -O /tmp/annonars-clinvar-minimal-grch38-20230910+0.18.0.tar.gz \
https://github.com/bihealth/annonars-data-clinvar/releases/download/clinvar-weekly-20230910/annonars-clinvar-minimal-grch38-20230910+0.18.0.tar.gz
wget -O /tmp/annonars-clinvar-minimal-grch37-20231015+0.24.1.tar.gz \
https://github.com/bihealth/annonars-data-clinvar/releases/download/annonars-data-clinvar-20231015/annonars-clinvar-minimal-grch37-20231015+0.24.1.tar.gz
wget -O /tmp/annonars-clinvar-minimal-grch38-20231015+0.24.1.tar.gz \
https://github.com/bihealth/annonars-data-clinvar/releases/download/annonars-data-clinvar-20231015/annonars-clinvar-minimal-grch38-20231015+0.24.1.tar.gz
tar --strip-components=2 -C .dev/volumes/varfish-static/data/download/annonars/ \
-xf /tmp/annonars-clinvar-minimal-grch37-20230910+0.18.0.tar.gz
tar --strip-components=2 -C .dev/volumes/varfish-static/data/download/annonars \
-xf /tmp/annonars-clinvar-minimal-grch38-20230910+0.18.0.tar.gz
tar -C .dev/volumes/varfish-static/data/download/annonars/ \
-tf /tmp/annonars-clinvar-minimal-grch37-20231015+0.24.1.tar.gz
tar -C .dev/volumes/varfish-static/data/download/annonars \
-xf /tmp/annonars-clinvar-minimal-grch38-20231015+0.24.1.tar.gz
ln -sr .dev/volumes/varfish-static/data/download/annonars/annonars-clinvar-minimal-grch37-20230910+0.18.0 \
rm -f .dev/volumes/varfish-static/data/annonars/grch37/clinvar
ln -sr .dev/volumes/varfish-static/data/download/annonars/annonars-clinvar-minimal-grch37-20231015+0.24.1 \
.dev/volumes/varfish-static/data/annonars/grch37/clinvar
ln -sr .dev/volumes/varfish-static/data/download/annonars/annonars-clinvar-minimal-grch38-20230910+0.18.0 \
rm -f .dev/volumes/varfish-static/data/annonars/grch38/clinvar
ln -sr .dev/volumes/varfish-static/data/download/annonars/annonars-clinvar-minimal-grch38-20231015+0.24.1 \
.dev/volumes/varfish-static/data/annonars/grch38/clinvar
wget -O /tmp/annonars-clinvar-genes-20230910+0.18.0.tar.gz \
https://github.com/bihealth/annonars-data-clinvar/releases/download/clinvar-weekly-20230910/annonars-clinvar-genes-20230910+0.18.0.tar.gz
wget -O /tmp/annonars-clinvar-genes-20231015+0.24.1.tar.gz \
https://github.com/bihealth/annonars-data-clinvar/releases/download/annonars-data-clinvar-20231015/annonars-clinvar-genes-20231015+0.24.1.tar.gz
tar -C .dev/volumes/varfish-static/data/download/annonars \
-xf /tmp/annonars-clinvar-genes-20230910+0.18.0.tar.gz
-xf /tmp/annonars-clinvar-genes-20231015+0.24.1.tar.gz
ln -sr .dev/volumes/varfish-static/data/download/annonars/annonars-clinvar-genes-20230910+0.18.0 \
rm -f .dev/volumes/varfish-static/data/annonars/clinvar-genes
ln -sr .dev/volumes/varfish-static/data/download/annonars/annonars-clinvar-genes-20231015+0.24.1 \
.dev/volumes/varfish-static/data/annonars/clinvar-genes
```
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