labman

lab manager for plate maps and sequence flows

Install

Labman relies on the Qiita database. You will need first to install Qiita in a different environment (Qiita is Python 2 only, while labman is Python 3) and create the Qiita database using the [Qiita installation instructions] (https://github.com/biocore/qiita/blob/master/INSTALL.md).

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

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

and then cloning the labman repository:

git clone https://github.com/jdereus/labman.git

You can then install labman by simply running:

pip install -e .

Configure labman by running labman config and answer to the configuration questions:

labman config
Path to the configuration file [~/.labman.cfg]:
Main configuration:
Test environment [True]:
Postgres configuration:
Postgres host [localhost]:
Postgres port [5432]:
Database name [qiita]:
Postgres user [labman]:
Postgres user password []:
Postgres admin user [labman]:
Postgres admin user password []:
Qiita configuration (for testing purposes):
Qiita server certificate []: /PATH/TO/qiita_core/support_files/server.crt

Finally, apply the SQL patches in the Qiita database so the labman structures are created:

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

Labman is now ready to run. Start the labman server with:

labman start_webserver

If it is running successfully, you will see the message Labman started on port 8080.