biocompute-objects / BCO_Documentation

Repository for documentation to support the IEEE 2791-2020 standard. Please see our home page for communications/publications:
http://biocomputeobject.org/
BSD 3-Clause "New" or "Revised" License
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Execution domain: different environmental variables #83

Closed jiugeyang closed 2 years ago

jiugeyang commented 4 years ago

Hi everyone,

An issue came to me when I was developing a future BCO. The current specification documents (quoted below) only give instructions on how to document a single set of environmental variables in the execution domain.

{"environment_variables": {
            "HOSTTYPE": "x86_64-linux",
            "EDITOR": "vim"
        }
 }

However, if a pipeline were executed on multiple platforms(e.g.HIVE one and HIVE AWS), there would be two or more different sets of environmental variables. How would these environmental variables be documented? Please let me know. Thanks!

HadleyKing commented 2 years ago

We should develop a response to this and include in the FAQ release for March

HadleyKing commented 2 years ago

Since the environment_variables is essentially free text a BCO writer could represent that any way they choose, but my recommendation would be to do something like the following:


{"environment_variables": {
            "HOSTTYPE_local": "x86_64-linux",
            "EDITOR_local": "vim",
            "HOSTTYPE_AWS": "x86_64-linux",
            "EDITOR_AWS": "vim"
        }
 }