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docs: bump clinvar version for annonars (#34)
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holtgrewe authored Nov 23, 2023
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26 changes: 14 additions & 12 deletions README.md
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Expand Up @@ -263,35 +263,37 @@ varfish-server-worker db to-bin \
```
To obtain ClinVar
Note that this will install the data from November 12, 2023 and you might want to [look here for the latest release](https://github.com/bihealth/annonars-data-clinvar/releases).
```bash session
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
wget -O /tmp/annonars-clinvar-minimal-grch37-20231112+0.25.0.tar.gz \
https://github.com/bihealth/annonars-data-clinvar/releases/download/annonars-data-clinvar-20231112/annonars-clinvar-minimal-grch37-20231112+0.25.0.tar.gz
wget -O /tmp/annonars-clinvar-minimal-grch38-20231112+0.25.0.tar.gz \
https://github.com/bihealth/annonars-data-clinvar/releases/download/annonars-data-clinvar-20231112/annonars-clinvar-minimal-grch38-20231112+0.25.0.tar.gz
tar -C .dev/volumes/varfish-static/data/download/annonars/ \
-tf /tmp/annonars-clinvar-minimal-grch37-20231015+0.24.1.tar.gz
-xf /tmp/annonars-clinvar-minimal-grch37-20231112+0.25.0.tar.gz
tar -C .dev/volumes/varfish-static/data/download/annonars \
-xf /tmp/annonars-clinvar-minimal-grch38-20231015+0.24.1.tar.gz
-xf /tmp/annonars-clinvar-minimal-grch38-20231112+0.25.0.tar.gz
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 \
ln -sr .dev/volumes/varfish-static/data/download/annonars/annonars-clinvar-minimal-grch37-20231112+0.25.0 \
.dev/volumes/varfish-static/data/annonars/grch37/clinvar
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 \
ln -sr .dev/volumes/varfish-static/data/download/annonars/annonars-clinvar-minimal-grch38-20231112+0.25.0 \
.dev/volumes/varfish-static/data/annonars/grch38/clinvar
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
wget -O /tmp/annonars-clinvar-genes-20231112+0.25.0.tar.gz \
https://github.com/bihealth/annonars-data-clinvar/releases/download/annonars-data-clinvar-20231112/annonars-clinvar-genes-20231112+0.25.0.tar.gz
tar -C .dev/volumes/varfish-static/data/download/annonars \
-xf /tmp/annonars-clinvar-genes-20231015+0.24.1.tar.gz
-xf /tmp/annonars-clinvar-genes-20231112+0.25.0.tar.gz
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 \
ln -sr .dev/volumes/varfish-static/data/download/annonars/annonars-clinvar-genes-20231112+0.25.0 \
.dev/volumes/varfish-static/data/annonars/clinvar-genes
```
### Setup Configuration
The next step step is to create the configuration files in `.dev/config`.
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