diff --git a/docs/source/install.rst b/docs/source/install.rst index c6c66977..547b7054 100644 --- a/docs/source/install.rst +++ b/docs/source/install.rst @@ -42,9 +42,9 @@ Cool-Seq-Tool requires an available instance of the Universal Transcript Archive export UTA_VERSION=uta_20210129b.pgd.gz # most recent as of 2023/12/05 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 5433 + 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 5433, 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_20210129b``. Set up SeqRepo -------------- diff --git a/docs/source/usage.rst b/docs/source/usage.rst index d717659a..1920a12c 100644 --- a/docs/source/usage.rst +++ b/docs/source/usage.rst @@ -101,7 +101,7 @@ 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 `_, i.e. of the form ``postgresql://:@://``, used by the :py:class:`cool_seq_tool.sources.uta_database.UtaDatabase` class. By default, it is set to ``postgresql://uta_admin:uta@localhost:5433/uta/uta_20210129b``. + - A `libpq connection string `_, i.e. of the form ``postgresql://:@://``, used by the :py:class:`cool_seq_tool.sources.uta_database.UtaDatabase` class. By default, it is set to ``postgresql://uta_admin:uta@localhost:5432/uta/uta_20210129b``. * - ``LIFTOVER_CHAIN_37_TO_38`` - A path to a `chainfile `_ for lifting from GRCh37 to GRCh38. Used by :py:class:`cool_seq_tool.sources.uta_database.UtaDatabase` 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 4ff5e3de..2a622e05 100644 --- a/src/cool_seq_tool/sources/uta_database.py +++ b/src/cool_seq_tool/sources/uta_database.py @@ -24,7 +24,7 @@ LIFTOVER_CHAIN_38_TO_37 = environ.get("LIFTOVER_CHAIN_38_TO_37") UTA_DB_URL = environ.get( - "UTA_DB_URL", "postgresql://uta_admin:uta@localhost:5433/uta/uta_20210129b" + "UTA_DB_URL", "postgresql://uta_admin:uta@localhost:5432/uta/uta_20210129b" ) logger = logging.getLogger(__name__) diff --git a/src/cool_seq_tool/version.py b/src/cool_seq_tool/version.py index b8b2f532..0ffdb5fe 100644 --- a/src/cool_seq_tool/version.py +++ b/src/cool_seq_tool/version.py @@ -1,2 +1,2 @@ """Define package version.""" -__version__ = "0.4.0-dev3" +__version__ = "0.4.0-dev4"