diff --git a/README.md b/README.md index 63e0c80..6daac38 100644 --- a/README.md +++ b/README.md @@ -60,7 +60,7 @@ Next, create a `docker-compose.override.yml` with the contents of the file `dock This will disable everything that we assume is running on your host when you are developing. This includes the REEV backend, redis, celery workers, postgres. -```bash session +``bash session cp docker-compose.override.yml-dev docker-compose.override.yml ``` @@ -77,7 +77,7 @@ full/annonars/gnomad-mtdna-grch37-3.1+0.12.8/*:annonars/gnomad-mtdna-grch37-3.1+ full/annonars/gnomad-mtdna-grch38-3.1+0.12.8/*:annonars/gnomad-mtdna-grch38-3.1+0.12.8 full/annonars/helixmtdb-grch37-20200327+0.12.8/*:annonars/helixmtdb-grch37-20200327+0.12.8 full/annonars/helixmtdb-grch38-20200327+0.12.8/*:annonars/helixmtdb-grch38-20200327+0.12.8 -full/annonars/genes-3.1+2.1.1+4.4+20230606+10.1+20230828+0.16.0/*:annonars/genes-3.1+2.1.1+4.4+20230606+10.1+20230828+0.16.0 +full/annonars/genes-3.1+2.1.1+4.4+20230606+10.1+20230828+0.19.0/*:annonars/genes-3.1+2.1.1+4.4+20230606+10.1+20230828+0.19.0 full/mehari/genes-txs-grch37-0.2.2/*:mehari/genes-txs-grch37-0.2.2 full/mehari/genes-txs-grch38-0.2.2/*:mehari/genes-txs-grch38-0.2.2 full/mehari/genes-xlink-20230624/*:mehari/genes-xlink-20230624 @@ -263,20 +263,28 @@ reev-server-worker db to-bin \ To obtain ClinVar ```bash session -wget -O /tmp/clinvar-annonars-rocksdb-grch37-20230826+0.6.3+0.12.9.tar.gz \ - https://github.com/bihealth/annonars-data-clinvar/releases/download/clinvar-weekly-20230826/clinvar-annonars-rocksdb-grch37-20230826+0.6.3+0.12.9.tar.gz -wget -O /tmp/clinvar-annonars-rocksdb-grch38-20230826+0.6.3+0.12.9.tar.gz \ - https://github.com/bihealth/annonars-data-clinvar/releases/download/clinvar-weekly-20230826/clinvar-annonars-rocksdb-grch38-20230826+0.6.3+0.12.9.tar.gz +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 -tar -C .dev/volumes/reev-static/data/download/annonars/ \ - -xf /tmp/clinvar-annonars-rocksdb-grch37-20230826+0.6.3+0.12.9.tar.gz -tar -C .dev/volumes/reev-static/data/download/annonars \ - -xf /tmp/clinvar-annonars-rocksdb-grch38-20230826+0.6.3+0.12.9.tar.gz +tar --strip-components=2 -C .dev/volumes/reev-static/data/download/annonars/ \ + -xf /tmp/annonars-clinvar-minimal-grch37-20230910+0.18.0.tar.gz +tar --strip-components=2 -C .dev/volumes/reev-static/data/download/annonars \ + -xf /tmp/annonars-clinvar-minimal-grch38-20230910+0.18.0.tar.gz -ln -sr .dev/volumes/reev-static/data/download/annonars/clinvar-annonars-rocksdb-grch37-20230826+0.6.3+0.12.9 \ +ln -sr .dev/volumes/reev-static/data/download/annonars/annonars-clinvar-minimal-grch37-20230910+0.18.0 \ .dev/volumes/reev-static/data/annonars/grch37/clinvar -ln -sr .dev/volumes/reev-static/data/download/annonars/clinvar-annonars-rocksdb-grch37-20230826+0.6.3+0.12.9 \ +ln -sr .dev/volumes/reev-static/data/download/annonars/annonars-clinvar-minimal-grch38-20230910+0.18.0 \ .dev/volumes/reev-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 +tar -C .dev/volumes/reev-static/data/download/annonars \ + -xf /tmp/annonars-clinvar-genes-20230910+0.18.0.tar.gz + +ln -sr .dev/volumes/reev-static/data/download/annonars/annonars-clinvar-genes-20230910+0.18.0 \ + .dev/volumes/reev-static/data/annonars/clinvar-genes ``` ### Setup Configuration @@ -293,7 +301,7 @@ Now, you can bring up the docker compose environment (stop with `Ctrl+C`). ```bash session docker compose up -``` +``- To verify the results, have a look at the following URLs: