diff --git a/docs/source/install.rst b/docs/source/install.rst index a51fc1d..709ca45 100644 --- a/docs/source/install.rst +++ b/docs/source/install.rst @@ -40,11 +40,11 @@ Cool-Seq-Tool requires an available instance of the Universal Transcript Archive createuser -U postgres anonymous createdb -U postgres -O uta_admin uta - export UTA_VERSION=uta_20210129b.pgd.gz # most recent as of 2023/12/05 + export UTA_VERSION=uta_20241220.pgd.gz # most recent as of 2025/03/10 curl -O https://dl.biocommons.org/uta/$UTA_VERSION gzip -cdq ${UTA_VERSION} | psql -h localhost -U uta_admin --echo-errors --single-transaction -v ON_ERROR_STOP=1 -d uta -p 5432 -By default, Cool-Seq-Tool expects to connect to the UTA database via a PostgreSQL connection served local on port 5432, under the PostgreSQL username ``uta_admin`` and the schema ``uta_20210129b``. +By default, Cool-Seq-Tool expects to connect to the UTA database via a PostgreSQL connection served local on port 5432, under the PostgreSQL username ``uta_admin`` and the schema ``uta_20241220``. Set up SeqRepo -------------- @@ -56,20 +56,20 @@ Cool-Seq-Tool requires access to `SeqRepo '/usr/local/share/seqrepo/2021-01-29' + PermissionError: [Error 13] Permission denied: '/usr/local/share/seqrepo/2024-12-20._fkuefgd' -> '/usr/local/share/seqrepo/2024-12-20' Try moving data manually with ``sudo``: diff --git a/docs/source/usage.rst b/docs/source/usage.rst index 161a571..d335c14 100644 --- a/docs/source/usage.rst +++ b/docs/source/usage.rst @@ -80,7 +80,7 @@ Individual classes will accept arguments upon initialization to set parameters r * - ``SEQREPO_ROOT_DIR`` - Path to SeqRepo directory (i.e. contains ``aliases.sqlite3`` database file, and ``sequences`` directory). Used by :py:class:`SeqRepoAccess `. If not defined, defaults to ``/usr/local/share/seqrepo/latest``. * - ``UTA_DB_URL`` - - A `libpq connection string `_, i.e. of the form ``postgresql://:@://``, used by the :py:class:`UtaDatabase ` class. By default, it is set to ``postgresql://uta_admin:uta@localhost:5432/uta/uta_20210129b``. + - A `libpq connection string `_, i.e. of the form ``postgresql://:@://``, used by the :py:class:`UtaDatabase ` class. By default, it is set to ``postgresql://uta_admin:uta@localhost:5432/uta/uta_20241220``. * - ``LIFTOVER_CHAIN_37_TO_38`` - A path to a `chainfile `_ for lifting from GRCh37 to GRCh38. Used by the :py:class:`LiftOver ` class as input to `agct `_. If not provided, agct will fetch it automatically from UCSC. * - ``LIFTOVER_CHAIN_38_TO_37`` diff --git a/src/cool_seq_tool/sources/uta_database.py b/src/cool_seq_tool/sources/uta_database.py index 71d9968..e369fae 100644 --- a/src/cool_seq_tool/sources/uta_database.py +++ b/src/cool_seq_tool/sources/uta_database.py @@ -27,7 +27,7 @@ UTADatabaseType = TypeVar("UTADatabaseType", bound="UtaDatabase") UTA_DB_URL = environ.get( - "UTA_DB_URL", "postgresql://uta_admin:uta@localhost:5432/uta/uta_20210129b" + "UTA_DB_URL", "postgresql://uta_admin:uta@localhost:5432/uta/uta_20241220" ) _logger = logging.getLogger(__name__)