Last update: 7/08/2020.
This is the documenation for the NMDC workflows. The latest version of this documenation can be found from here.
This documentation is written in reStructuredText with Sphinx. It can be compiled to PDF, HTML and other formats.
To compile a PDF run this command in Terminal:
`python compose.py`
This command will pull down the NMDC workflows, whose repositories are defined in the nmdc_doc.yaml file. It will extract docs/*.rst files from individual workflows and put them (alone with referenced png graphics if any) into the _doc directory. The assumpution is that all NMDC workflows follows the directory conversion (/docs) for documentation and only one rst file is used.
Then go to the _doc directory and use the following commaand to generate PDF documentation:
make pdflatex
The result pdf file is located at docs/_build/latex/NMDCWorkflows.pdf
You can also run this single command in the root directory of this repository:
`python compose.py && cd docs && make latexpdf`
You can also run this single command in the root directory of this repository:
`python compose.py && cd docs && make html`
An on-line version of the documentation is available here.
New workflow documentations can be added easily by editing the "nmdc_doc.yaml" file. For example to add the metaproteomics workflow documentation, one just need to add the follolwing line under the *workflow* section:
'5_Metaproteomics': 'https://github.com/microbiomedata/metaPro'
Note that the first item is the workflow name the value string after it is URL to the repository of this workflow.
The workflows section now looks like this:
'1_RQC': 'https://github.com/microbiomedata/ReadsQC'
'2_MAG': 'https://github.com/microbiomedata/metaMAGs.git'
'3_MetaGAssemly': 'https://github.com/microbiomedata/metaAssembly.git'
'4_MetaGAnnotation': 'https://github.com/microbiomedata/mg_annotation.git'
'5_Metaproteomics': 'https://github.com/microbiomedata/metaPro'