LabControl

lab manager for plate maps and sequence flows

Install

LabControl relies on the Qiita database and webserver. You will need first to install Qiita in a different environment than LabControl using the Qiita installation instructions.
(It is also necessary to start the qiita webserver on port 8383, rather than the default port for qiita of 21174; this can be done with the command qiita pet webserver start --port 8383 .) The instructions below assume the Qiita PostgreSQL database is named qiita_test, which is the default name of the database created by the Qiita installation process; if your Qiita installation has a different database name, substitute that for qiita_test throughout.

Once Qiita is installed, create a new, empty conda environment for LabControl. Source this environment and install LabControl; start by first installing the qiita_client library:

pip install https://github.com/qiita-spots/qiita_client/archive/master.zip

and then cloning the LabControl repository:

git clone https://github.com/biocore/LabControl.git

You can then install LabControl by simply running:

pip install -e .

Generate a certificate for HTTPS (note that the below command uses default values, but of course we suggest changing them):

mkdir -p support_files
openssl req -x509 -nodes -days 365 -newkey rsa:2048 \
    -keyout support_files/server.key \
    -out support_files/server.crt \
    -subj "/C=US/ST=CA/L=LaJolla/O=/CN=localhost"

Configure LabControl by running labcontrol config and answer to the configuration questions:

Path to the configuration file [~/.labcontrol.cfg]:
Main configuration:
Test environment [True]:
Log directory [/tmp/]:
LabControl Certificate Filepath []: /PATH/TO/labcontrol/support_files/server.crt
LabControl Key Filepath []: /PATH/TO/labcontrol/support_files/server.key
Server cookie secret (default: random) ['random-key']:
Postgres configuration:
Postgres host [localhost]:
Postgres port [5432]:
Database name [qiita]:
Postgres user [labcontrol]:
Postgres user password []:
Postgres admin user [labcontrol]:
Postgres admin user password []:
Qiita configuration (for testing purposes):
Qiita server certificate []: /PATH/TO/qiita_core/support_files/server.crt

Apply the SQL patches in the Qiita database so the basic LabControl structures are created:

psql -d qiita_test -f labcontrol/db/support_files/db_patch.sql
psql -d qiita_test -f labcontrol/db/support_files/db_patch_manual.sql

If creating a development environment for LabControl, then run:

psql -d qiita_test -f labcontrol/db/support_files/populate_test_db.sql

to set up the database to support running the unit tests. Alternately, if creating a production or production-like environment, run:

psql -d qiita_test -f labcontrol/db/support_files/populate_prod_db.sql

Note that the postgres user specified for the LabControl software (labcontrol in the config example above) must be granted "select" permissions on all tables in the "qiita" schema and "all" permissions on all tables in the "labcontrol" schema, as well as being the owner of all tables in the "labcontrol" schema.
These ownerships and permissions can be granted with SQL like that shown below, after setting the USER variable to be the postgres user specified for the LabControl software and DB to be the database name for your Qiita installation:

USER=labcontrol
DB=qiita_test
SCHEMA=labcontrol
for table in `psql -tc "select tablename from pg_tables where schemaname = '${SCHEMA}';" ${DB}` ; do psql -c "alter table ${SCHEMA}.${table} owner to ${USER}" ${DB}; done
psql -d qiita-test -c "Grant select on all tables in schema qiita to ${USER};"
psql -d qiita-test -c "Grant all on all tables in schema labcontrol to ${USER};"

LabControl is now ready to run. Start the LabControl server with:

labcontrol start-webserver

If it is running successfully, you will see the message LabControl started on port 8181. Note that by default, LabControl starts on port 8181; if you would like to start it on a different port, use the optional --port switch, as shown in the below example to start it on port 5555:

labcontrol start-webserver --port 5555