diff --git a/README.md b/README.md index a37d72f3..5edf0356 100644 --- a/README.md +++ b/README.md @@ -18,7 +18,7 @@ cd fusion-curation Ensure that the following data sources are available: - the [VICC Gene Normalization](https://github.com/cancervariants/gene-normalization) database, accessible from a DynamoDB-compliant service. Set the endpoint address with environment variable `GENE_NORM_DB_URL`; default value is `http://localhost:8000`. -- the [Biocommons SeqRepo](https://github.com/biocommons/biocommons.seqrepo) database. Provide local path with environment variable `SEQREPO_DATA_PATH`; default value is `/usr/local/share/seqrepo/latest`. +- the [Biocommons SeqRepo](https://github.com/biocommons/biocommons.seqrepo) database, used by `Cool-Seq-Tool`. The precise file location is configurable via the `SEQREPO_ROOT_DIR` variable, per the [documentation](https://coolseqtool.readthedocs.io/0.6.0/usage.html#environment-configuration). - the [Biocommons Universal Transcript Archive](https://github.com/biocommons/uta), by way of Genomic Med Lab's [Cool Seq Tool](https://github.com/GenomicMedLab/cool-seq-tool) package. Connection parameters to the Postgres database are set most easily as a [Libpq-compliant URL](https://www.postgresql.org/docs/current/libpq-connect.html#LIBPQ-CONNSTRING) under the environment variable `UTA_DB_URL`. Create a virtual environment for the server and install. Note: there's also a Pipfile so you can skip the virtualenv steps if you'd rather use a Pipenv instance instead of virtualenv/venv. I have been sticking with the latter because [Pipenv doesn't play well with entry points in development](https://stackoverflow.com/a/69225249), but if you aren't editing them in `setup.cfg`, then the former should be fine. diff --git a/server/src/curfu/__init__.py b/server/src/curfu/__init__.py index bb833ca9..7a993d75 100644 --- a/server/src/curfu/__init__.py +++ b/server/src/curfu/__init__.py @@ -50,9 +50,6 @@ else: UTA_DB_URL = "postgresql://uta_admin@localhost:5433/uta/uta_20210129" -# get local seqrepo location -SEQREPO_DATA_PATH = environ.get("SEQREPO_DATA_PATH", f"{APP_ROOT}/data/seqrepo/latest") - class LookupServiceError(Exception): """Custom Exception to use when lookups fail in curation services."""