fix: Correct the entrypoint command

[gromdimon]

While running the annonars service in reev-docker-compose suite, the following error was encountered:

annonars  | + set -euo pipefail
annonars  | + PATH_DB_BASE=/data/annonars
annonars  | + HTTP_HOST=0.0.0.0
annonars  | + HTTP_PORT=8080
annonars  | + PATH_DB_CLINVAR_37=/data/annonars/grch37/clinvar/rocksdb
annonars  | + PATH_DB_CLINVAR_38=/data/annonars/grch38/clinvar/rocksdb
annonars  | + PATH_DB_CLINVAR_SV_37=/data/annonars/grch37/clinvar-sv/rocksdb
annonars  | + PATH_DB_CLINVAR_SV_38=/data/annonars/grch38/clinvar-sv/rocksdb
annonars  | + PATH_DB_CADD_37=/data/annonars/grch37/cadd/rocksdb
annonars  | + PATH_DB_CADD_38=/data/annonars/grch38/cadd/rocksdb
annonars  | + PATH_DB_DBSNP_37=/data/annonars/grch37/dbsnp/rocksdb
annonars  | + PATH_DB_DBSNP_38=/data/annonars/grch38/dbsnp/rocksdb
annonars  | + PATH_DB_DBNSFP_37=/data/annonars/grch37/dbnsfp/rocksdb
annonars  | + PATH_DB_DBNSFP_38=/data/annonars/grch38/dbnsfp/rocksdb
annonars  | + PATH_DB_DBSCSNV_37=/data/annonars/grch37/dbscsnv/rocksdb
annonars  | + PATH_DB_DBSCSNV_38=/data/annonars/grch38/dbscsnv/rocksdb
annonars  | + PATH_DB_GNOMAD_MTDNA_37=/data/annonars/grch37/gnomad-mtdna/rocksdb
annonars  | + PATH_DB_GNOMAD_MTDNA_38=/data/annonars/grch38/gnomad-mtdna/rocksdb
annonars  | + PATH_DB_GNOMAD_EXOMES_37=/data/annonars/grch37/gnomad-exomes/rocksdb
annonars  | + PATH_DB_GNOMAD_EXOMES_38=/data/annonars/grch38/gnomad-exomes/rocksdb
annonars  | + PATH_DB_GNOMAD_GENOMES_37=/data/annonars/grch37/gnomad-genomes/rocksdb
annonars  | + PATH_DB_GNOMAD_GENOMES_38=/data/annonars/grch38/gnomad-genomes/rocksdb
annonars  | + PATH_DB_HELIXMTDB_37=/data/annonars/grch37/helixmtdb/rocksdb
annonars  | + PATH_DB_HELIXMTDB_38=/data/annonars/grch38/helixmtdb/rocksdb
annonars  | + PATH_DB_CONS_37=/data/annonars/grch37/cons/rocksdb
annonars  | + PATH_DB_CONS_38=/data/annonars/grch38/cons/rocksdb
annonars  | + PATH_GENES=/data/annonars/genes/rocksdb
annonars  | + PATH_GENES_CLINVAR=/data/annonars/clinvar-genes/rocksdb
annonars  | + first=
annonars  | + '[' '' == exec ']'
annonars  | ++ test -e /data/annonars/grch37/clinvar/rocksdb
annonars  | ++ echo --path-clinvar /data/annonars/grch37/clinvar/rocksdb
annonars  | ++ test -e /data/annonars/grch38/clinvar/rocksdb
annonars  | ++ echo --path-clinvar /data/annonars/grch38/clinvar/rocksdb
annonars  | ++ test -e /data/annonars/grch37/clinvar-sv/rocksdb
annonars  | ++ echo --path-clinvar-sv /data/annonars/grch37/clinvar-sv/rocksdb
annonars  | ++ test -e /data/annonars/grch38/clinvar-sv/rocksdb
annonars  | ++ echo --path-clinvar-sv /data/annonars/grch38/clinvar-sv/rocksdb
annonars  | ++ test -e /data/annonars/grch37/cadd/rocksdb
annonars  | ++ echo --path-cadd /data/annonars/grch37/cadd/rocksdb
annonars  | ++ test -e /data/annonars/grch38/cadd/rocksdb
annonars  | ++ echo --path-cadd /data/annonars/grch38/cadd/rocksdb
annonars  | ++ test -e /data/annonars/grch37/dbsnp/rocksdb
annonars  | ++ echo --path-dbsnp /data/annonars/grch37/dbsnp/rocksdb
annonars  | ++ test -e /data/annonars/grch38/dbsnp/rocksdb
annonars  | ++ echo --path-dbsnp /data/annonars/grch38/dbsnp/rocksdb
annonars  | ++ test -e /data/annonars/grch37/dbnsfp/rocksdb
annonars  | ++ echo --path-dbnsfp /data/annonars/grch37/dbnsfp/rocksdb
annonars  | ++ test -e /data/annonars/grch38/dbnsfp/rocksdb
annonars  | ++ echo --path-dbnsfp /data/annonars/grch38/dbnsfp/rocksdb
annonars  | ++ test -e /data/annonars/grch37/dbscsnv/rocksdb
annonars  | ++ echo --path-dbscsnv /data/annonars/grch37/dbscsnv/rocksdb
annonars  | ++ test -e /data/annonars/grch38/dbscsnv/rocksdb
annonars  | ++ echo --path-dbscsnv /data/annonars/grch38/dbscsnv/rocksdb
annonars  | ++ test -e /data/annonars/grch37/gnomad-mtdna/rocksdb
annonars  | ++ echo --path-gnomad-mtdna /data/annonars/grch37/gnomad-mtdna/rocksdb
annonars  | ++ test -e /data/annonars/grch38/gnomad-mtdna/rocksdb
annonars  | ++ echo --path-gnomad-mtdna /data/annonars/grch38/gnomad-mtdna/rocksdb
annonars  | ++ test -e /data/annonars/grch37/gnomad-exomes/rocksdb
annonars  | ++ echo --path-gnomad-exomes /data/annonars/grch37/gnomad-exomes/rocksdb
annonars  | ++ test -e /data/annonars/grch38/gnomad-exomes/rocksdb
annonars  | ++ echo --path-gnomad-exomes /data/annonars/grch38/gnomad-exomes/rocksdb
annonars  | ++ test -e /data/annonars/grch37/gnomad-genomes/rocksdb
annonars  | ++ echo --path-gnomad-genomes /data/annonars/grch37/gnomad-genomes/rocksdb
annonars  | ++ test -e /data/annonars/grch38/gnomad-genomes/rocksdb
annonars  | ++ echo --path-gnomad-genomes /data/annonars/grch38/gnomad-genomes/rocksdb
annonars  | ++ test -e /data/annonars/grch37/helixmtdb/rocksdb
annonars  | ++ echo --path-helixmtdb /data/annonars/grch37/helixmtdb/rocksdb
annonars  | ++ test -e /data/annonars/grch38/helixmtdb/rocksdb
annonars  | ++ echo --path-helixmtdb /data/annonars/grch38/helixmtdb/rocksdb
annonars  | ++ test -e /data/annonars/grch37/cons/rocksdb
annonars  | ++ echo --path-ucsc-conservation /data/annonars/grch37/cons/rocksdb
annonars  | ++ test -e /data/annonars/grch38/cons/rocksdb
annonars  | ++ echo --path-ucsc-conservation /data/annonars/grch38/cons/rocksdb
annonars  | ++ test -e /data/annonars/genes/rocksdb
annonars  | ++ echo --path-genes /data/annonars/genes/rocksdb
annonars  | ++ test -e /data/annonars/clinvar-genes/rocksdb
annonars  | ++ echo --path-clinvar-genes /data/annonars/clinvar-genes/rocksdb
annonars  | + exec annonars run-server --path-clinvar /data/annonars/grch37/clinvar/rocksdb --path-clinvar /data/annonars/grch38/clinvar/rocksdb --path-clinvar-sv /data/annonars/grch37/clinvar-sv/rocksdb --path-clinvar-sv /data/annonars/grch38/clinvar-sv/rocksdb --path-cadd /data/annonars/grch37/cadd/rocksdb --path-cadd /data/annonars/grch38/cadd/rocksdb --path-dbsnp /data/annonars/grch37/dbsnp/rocksdb --path-dbsnp /data/annonars/grch38/dbsnp/rocksdb --path-dbnsfp /data/annonars/grch37/dbnsfp/rocksdb --path-dbnsfp /data/annonars/grch38/dbnsfp/rocksdb --path-dbscsnv /data/annonars/grch37/dbscsnv/rocksdb --path-dbscsnv /data/annonars/grch38/dbscsnv/rocksdb --path-gnomad-mtdna /data/annonars/grch37/gnomad-mtdna/rocksdb --path-gnomad-mtdna /data/annonars/grch38/gnomad-mtdna/rocksdb --path-gnomad-exomes /data/annonars/grch37/gnomad-exomes/rocksdb --path-gnomad-exomes /data/annonars/grch38/gnomad-exomes/rocksdb --path-gnomad-genomes /data/annonars/grch37/gnomad-genomes/rocksdb --path-gnomad-genomes /data/annonars/grch38/gnomad-genomes/rocksdb --path-helixmtdb /data/annonars/grch37/helixmtdb/rocksdb --path-helixmtdb /data/annonars/grch38/helixmtdb/rocksdb --path-ucsc-conservation /data/annonars/grch37/cons/rocksdb --path-ucsc-conservation /data/annonars/grch38/cons/rocksdb --path-genes /data/annonars/genes/rocksdb --path-clinvar-genes /data/annonars/clinvar-genes/rocksdb --listen-host 0.0.0.0 --listen-port 8080
annonars  | error: unrecognized subcommand 'run-server'
annonars  |
annonars  |   tip: a similar subcommand exists: 'server'
annonars  |
annonars  | Usage: annonars [OPTIONS] <COMMAND>
annonars  |
annonars  | For more information, try '--help'.

The provided fix worked for me. Please, review and merge as needed.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 73.14%. Comparing base (64aa6a4) to head (de5d89c).
Report is 8 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #541   +/-   ##
=======================================
  Coverage   73.14%   73.14%           
=======================================
  Files          79       79           
  Lines        8199     8199           
=======================================
  Hits         5997     5997           
  Misses       2202     2202           

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[gromdimon]

@holtgrewe since I'm not an expert in rust, I can't be sure, that this is the right fix. Also note, that docker build workflow failed just because the fork doesn't have permission for push to the container registry. The actual docker container was successfully built.

[holtgrewe]

Looks good in general. But you will also need to update all data. See updates to the download script in varfish docker compose.