corilo/enviroms repository overview

⁠Table of Contents

• Introduction
  • EnviroMS⁠
  • Version⁠
  • Data Input⁠
  • Data Output⁠
  • Data Structure⁠
  • Features⁠
  • Code Documentation⁠
• Installation
  • PyPi⁠
• Execution:
  • CLI⁠
  • MiniWDL⁠
  • Docker Container⁠

⁠EnviroMS

EnviroMS is a workflow for natural organic matter data processing and annotation

⁠Current Version

⁠4.1.5

⁠Data input formats

• Generic mass list in profile and centroid mode (include all delimiters types and Excel formats)

⁠Data output formats

• Pandas data frame (can be saved using pickle, h5, etc)
• Text Files (.csv, tab separated .txt, etc)
• Microsoft Excel (xlsx)
• Automatic JSON for workflow metadata
• Self-containing Hierarchical Data Format (.hdf5) including raw data and ime-series data-point for processed data-sets with all associated workflow metadata (JSON)

⁠Data structure types

• FT-ICR MS
• LC-FT-ICR MS

⁠Molecular formulae search and assignment

• Automatic local (SQLite) or external (PostgreSQL) database check, generation, and search
• Automatic molecular formulae assignments algorithm for ESI(-) MS for natural organic matter analysis
• Automatic fine isotopic structure calculation and search for all isotopes
• Flexible Kendrick normalization base
• Kendrick filter using density-based clustering
• Kendrick classification
• Hetero atoms classification and visualization

⁠EnviroMS Installation

• PyPi:

pip3 install enviroms

• From source:

pip3 install --editable .

To be able to open thermo raw files a installation of pythonnet is needed:

• Windows:

  pip3 install pythonnet
  

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• Mac and Linux:

  brew install mono
  pip3 install pythonnet   
  

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⁠Running the workflow

enviroMS dump-corems-enviroms-template EnviromsFile.json

enviroMS dump-corems-template CoremsFile.json

Modify the EnviromsFile.json and CoremsFile.json accordingly to your dataset and workflow parameters make sure to include CoremsFile.json path inside the EnviromsFile.json: "corems_json_path": "path_to_CoremsFile.json"

enviroMS run-di path_to_MetamsFile.json

⁠MiniWDL

• Change wdl/enviroms_input.json to specify the data location

• Change data/CoremsFile.json to specify the workflow parameters

Install miniWDL:

pip3 install miniwdl

Call:

miniwdl run wdl/enviroMS.wdl -i wdl/enviroms_input.json --verbose --no-cache --copy-input-files

WARNING ** Current mode only allows for multiprocessing in a single node and it defaults to one job at a time. To use multiprocessing mode modify the parameter "runDirectInfusion.jobs_count" in the enviroMS.wdl and modify the parameter "MolecularFormulaSearch.url_database" on CoremsFile.json to point to a Postgresql url. The default is set to use SQLite and it will fail on multiprocessing mode.

⁠EnviroMS Docker

A docker image containing the EnviroMS command line as code entry-point

If you don't have docker installed, the easiest way is to install docker for desktop⁠

• Pull from Docker Registry:

  docker pull corilo/enviroms:latest
  
  

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• Or to build the image from source:

  docker build -t enviroms:latest .
  

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• Run Workflow from Container:

  $(data_dir) = dir_containing the FT-ICR MS data, EnviromsFile.json and CoremsFile.json

  docker run -v $(data_dir):/enviroms/data corilo/enviroms:latest enviroMS run-di /enviroms/data/EnviromsFile.json    
  

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• Save a new parameters file template:

  docker run -v $(data_dir):/enviroms/data corilo/enviroms:latest enviroMS dump_json_template /enviroms/data/EnviromsFile.json    
  

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  docker run -v $(data_dir):/metaB/data corilo/enviroms:latest enviroMS dump_corems_json_template /metaB/data/CoremsFile.json
  

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⁠Disclaimer

This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, nor any jurisdiction or organization that has cooperated in the development of these materials, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, software, or process disclosed, or represents that its use would not infringe privately owned rights.

Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or Battelle Memorial Institute. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.

             PACIFIC NORTHWEST NATIONAL LABORATORY
                          operated by
                            BATTELLE
                            for the
               UNITED STATES DEPARTMENT OF ENERGY
                under Contract DE-AC05-76RL01830