Merge master into lipid_dev

docs/index.rst

@@ -1,33 +1,23 @@
+:github_url: https://github.com/microbiomedata/metaMS/blob/master/docs/index.rst
+
+..
+   Note: The above `github_url` field is used to force the target of the "Edit on GitHub" link
+         to be the specified URL. That makes it so the link will work, regardless of the Sphinx
+         site the file is incorporated into. You can learn more about the `github_url` field at:
+         https://sphinx-rtd-theme.readthedocs.io/en/stable/configuring.html#confval-github_url
+
 Metabolomics Workflow
 ==============================
 
-Summary
+.. image:: metams_workflow2024.svg
+
+Workflow Overview
 -------
 
 The gas chromatography-mass spectrometry (GC-MS) based metabolomics workflow (metaMS) has been developed by leveraging PNNL's CoreMS software framework.
 The current software design allows for the orchestration of the metabolite characterization pipeline, i.e., signal noise reduction, m/z based Chromatogram Peak Deconvolution,
 abundance threshold calculation, peak picking, spectral similarity calculation and molecular search, similarity score calculation, and confidence filtering, all in a single step.
 
-
-Workflow Diagram
-------------------
-
-.. image:: metamsworkflow.png
-
-
-Workflow Dependencies
----------------------
-
-Third party software
-~~~~~~~~~~~~~~~~~~~~
-
-- CoreMS (2-clause BSD)
-- Click (BSD 3-Clause "New" or "Revised" License)
-
-Database 
-~~~~~~~~~~~~~~~~
-- PNNL Metabolomics GC-MS Spectral Database
-
 Workflow Availability
 ---------------------
 
@@ -43,18 +33,47 @@ https://pypi.org/project/metaMS/
 The databases are available by request.
 Please contact NMDC ([email protected]) for access.
 
-Test datasets
--------------
-https://github.com/microbiomedata/metaMS/blob/master/data/GCMS_FAMES_01_GCMS-01_20191023.cdf
+Requirements for Execution
+--------------------------
 
+- Docker Container Runtime
+
+  or  
+- Python Environment >= 3.10
+- Python Dependencies are listed on requirements.txt
 
 Execution Details
----------------------
+~~~~~~~~~~~~~~~~
 
 Please refer to: 
 
 https://github.com/microbiomedata/metaMS#metams-installation
 
+Hardware Requirements
+--------------------------
+- To run this application, you need a processor with at least 2.0 GHz speed, 8GB of RAM, 10GB of free hard disk space
+
+
+Workflow Dependencies
+---------------------
+
+Software
+~~~~~~~~~~~~~~~~~~~~
+
+- CoreMS (2-clause BSD)
+- Click (BSD 3-Clause "New" or "Revised" License)
+
+Database
+~~~~~~~~~~~~~~~~
+- PNNL Internal Metabolomics GC-MS Spectral Database, version 20191015
+- Test database provided at db/EMSL_lowres_gcms_test_database.sqlite
+- Database will be provided via an API in FY25
+
+Test datasets
+-------------
+https://github.com/microbiomedata/metaMS/tree/master/data/raw_data/GCMS_FAMES_01_GCMS-01_20191023.cdf
+
+
 Inputs
 ~~~~~~~~
 
@@ -76,15 +95,6 @@ Outputs
 - Workflow Metadata:
     - JSON
 
-Requirements for Execution
---------------------------
-
-- Docker Container Runtime
-
-  or  
-- Python Environment >= 3.6
-- Python Dependencies are listed on requirements.txt
-
 
 Version History
 ---------------
@@ -94,4 +104,4 @@ Version History
 Point of contact
 ----------------
 
-Package maintainer: Yuri E. Corilo <[email protected]>
+Package maintainer: Yuri E. Corilo <[email protected]>