- Introduction
- Installation
- Execution:
EnviroMS is a workflow for natural organic matter data processing and annotation
- Generic mass list in profile and centroid mode (include all delimiters types and Excel 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)
- FT-ICR MS
- LC-FT-ICR MS
- 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
- PyPi:
pip3 install enviroms
- From source:
pip3 install --editable .
To be able to open thermo raw files a installation of pythonnet is needed:
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Windows:
pip3 install pythonnet
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Mac and Linux:
brew install mono pip3 install pythonnet
enviroMS dump-di-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_EnviromsFile.json
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Change wdl/enviroms_input.json to specify the data location
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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.
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
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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
docker run -v $(data_dir):/metaB/data corilo/enviroms:latest enviroMS dump_corems_json_template /metaB/data/CoremsFile.json
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