Skip to content

Latest commit

 

History

History
69 lines (49 loc) · 2.55 KB

database_list.rst

File metadata and controls

69 lines (49 loc) · 2.55 KB

database_list command

This section is auto-generated from the help text for the planemo command database_list. This help message can be generated with planemo database_list --help.

Usage:

planemo database_list [OPTIONS]

Help

List databases in configured database source.

Currently the only implementation is postgres which will be managed with psql.

Planemo database_ commands make it very easy to create and destroy databases, therefore it should not be used for production data - and it should not even be connnected to a production database server. Planemo is intended for development purposes only.

Planemo will assume that it can manage and access postgres databases without specifying a password. This can be accomplished by configuring postgres to not required a password for the planemo user or by specifying a password in a .pgpass file.

Planemo can be configured to not require a password for the planemo user in the postgres configuration file pg_hba.conf (on Ubuntu/Debian linux distros this file is in /etc/postgresql/<postgres_version>/main/ directory). Adding the following lines to that file will allow planemo and Galaxy to access the databases without a password.

# "local" is for Unix domain socket connections only
local   all   all                    trust
# IPv4 local connections:
host    all   all    127.0.0.1/32    trust
# IPv6 local connections:
host    all   all    ::1/128         trust

More information on the pg_hda.conf configuration file can be found at http://www.postgresql.org/docs/9.3/static/auth-pg-hba-conf.html.

Information on .pgpass files can be found at at the following location: http://www.postgresql.org/docs/9.4/static/libpq-pgpass.html. In Ubuntu and Debian distros - a postgres user likely already exists and its password can be set by setting up a file ~/.pgpass file with the following contents.

*:*:*:postgres:<postgres_password>

Options:

--postgres_psql_path TEXT      Name or or path to postgres client binary
                               (psql).
--postgres_database_user TEXT  Postgres username for managed development
                               databases.
--postgres_database_host TEXT  Postgres host name for managed development
                               databases.
--postgres_database_port TEXT  Postgres port for managed development
                               databases.
--help                         Show this message and exit.