lattice-tools

External scripts used to interact with the Lattice Database

Environment configuration

1. Create a virtual environment. This example uses anaconda. Other options would also work, like venv or pyenv

   conda create --name lattice_submit python=3.7
   

   You will need to be in this environment for the following instructions

   conda activate lattice_submit
   

Note: the examples call the environment lattice_submit but you can name it anything as long as it is clearly distinguishable from the enviroment you use to launch the encoded app

1. Install the following packages

   pip install requests openpyxl Pillow gspread gspread_formatting oauth2client scanpy
   

   pip install google-cloud-storage google-auth-httplib2
   

   pip install python-magic-bin==0.4.14
   

   conda install -c conda-forge anndata
   

   conda install -c conda-forge pint
   

   conda install pandas jsonschema
   

2. Define variables in your environment based on the various servers you might submit to based on an alias for each server (ALIAS_KEY, ALIAS_SECRET, ALIAS_SERVER). For example, when submitting to a local instance of the app, you might call this local.
   So you'd define the following three variables.

   $ conda env config vars set LOCAL_KEY=<key>

   $ conda env config vars set LOCAL_SECRET=<secret>

   $ conda env config vars set LOCAL_SERVER=http://localhost:6543

3. After defining those, you'll need to reactivate your environment

   conda activate lattice_submit
   

   You can then confirm that they are defined

   conda env config vars list
   

Available tools

• qcmetrics_reader.py Transforms quality metrics and other processing information from various files of a standard CellRanger outs/ directory into the Lattice schema

• checkfiles.py Gathers data file content information and compares with submitted metadata run instructions

• DCP_mapper.py Transforms a Lattice Dataset into HCA DCP-approved schema and stages at the DCP for submission to the HCA Portal run instructions

• flattener.py Transforms a contributor matrix, raw count data, and Lattice metadata into a cellxgene-approved matrix file run instructions

• make_template.py Produces a tabular representation of Lattice schema submittable properties, for ease of wrangling

• submit_metadata.py Transforms tabulated metadata into json objects and posts/patches to the Lattice DB use instructions