ProjMan Filler

App for filling ProjMan

Free software: GNU General Public License v3

Features

This program will fill the ProjMan database, based on the Stats.json and Interop files in an Illumina runfolder

Usage

To run projman_filler run:

export PROJMAN_DB="mssql+pymssql://<usernam>:<password>@<host>/<database>?charset=utf8"
projman_filler <path to the runfolder to insert into the db>

The location of the bcl2fastq statistics folder, i.e. where Stats.json is located, can be specified using the -b|--bcl2fastq-stats flag. Specify the location relative to the runfolder. Default: "Unaligned/Stats"

If the runfolder has already been loaded into the database, you can add the make projman_filler remove the old results and add the new once by adding the --force flag, i.e:

export PROJMAN_DB="mssql+pymssql://<usernam>:<password>@<host>/<database>?charset=utf8"
projman_filler --force <path to the runfolder to insert into the db>

For more flags, see cli.py.

Install instructions

Installing projman_filler can be done in the following way.

Please note that projman_filler uses python 3.6, ensure this is first installed.

Download the projman_filler delivery
Install projman_filler with pip as normal, i.e. pip install <path to source>

Development and testing

Set up a Python environment using the latest version of Python 3.6 (3.6.12 as of this writing).

Then run:

 pip install -e . -r requirements_dev.txt

To run the app locally:

export PROJMAN_DB="mssql+pymssql://<usernam>:<password>@<host>/<database>?charset=utf8"
&& python ./projman_filler/cli.py <path to the runfolder to insert into the db>

Run tests with:

 python setup.py pytest

Credits

This package was created with Cookiecutter_ and the audreyr/cookiecutter-pypackage_ project template.