Mercurial > repos > fubar > egapx_runner
changeset 6:a7304162d737 draft
planemo upload for repository https://github.com/ncbi/egapx commit 9e59da535540cb4d5c1c412bb2b0969744dfb0b0-dirty
| author | fubar |
|---|---|
| date | Sun, 04 Aug 2024 02:30:36 +0000 |
| parents | 6effccc966d0 |
| children | 9c778770514f |
| files | egapx_runner.xml |
| diffstat | 1 files changed, 16 insertions(+), 8 deletions(-) [+] |
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--- a/egapx_runner.xml Sun Aug 04 01:59:37 2024 +0000 +++ b/egapx_runner.xml Sun Aug 04 02:30:36 2024 +0000 @@ -15,9 +15,9 @@ <inputs> <param name="yamlconfig" type="data" optional="false" label="egapx configuration yaml file to execute" help="" format="yaml,txt" multiple="false"/> <param name="econfig" type="select" label="Workflow run configuration to suit the machine in use" help="Docker minimal will run the sample minimal dustmite yaml"> - <option value="docker_minimal">Docker_minimal supports only the minimal dust mite example yaml using 6GB and 4 cores</option> - <option value="singularity">Singularity requires at least 128GB ram and 32 cores. 256GB and 64 cores recommended</option> - <option value="docker">Docker requires at least 128GB ram and 32 cores. 256GB and 64 cores recommended</option> + <option value="docker_minimal">Docker_minimal: supports only the minimal dust mite example yaml using 6GB and 4 cores</option> + <option value="singularity">Singularity: requires at least 128GB ram and 32 cores. 256GB and 64 cores recommended</option> + <option value="docker">Docker: requires at least 128GB ram and 32 cores. 256GB and 64 cores recommended</option> </param> </inputs> <outputs> @@ -41,24 +41,32 @@ Galaxy tool wrapping the Eukaryotic Genome Annotation Pipeline (EGAPx) ================================================================================================= +.. class:: warningmark + **Proof of concept: a quick hack to run a NF workflow inside a specialised Galaxy tool wrapper** -EGAPx is a big, complicated Nextflow workflow, challenging and costly to re-implement **properly**, requiring dozens of new tools and complicated ``groovy`` WF logic. +EGAPx is a big, complicated Nextflow workflow, challenging and costly to re-implement **properly**, requiring dozens of new tools and replicating a lot of +complicated *groovy* workflow logic. -It is also very new and in rapid development. Investing that effort and keeping it updated as EGAPx changes rapidly may be *inefficient of developer resources*. +It is also very new and in rapid development. Investing developer effort and keeping updated as EGAPx changes rapidly may be *inefficient of developer resources*. This wrapper is designed to allow measuring how *inefficient* it is in terms of computing resource utilisation, in comparison to the developer effort required to convert Nextflow DDL into tools and WF logic. Balancing these competing requirements is a fundamental Galaxy challenge. -EGAPx requires huge resources to run with useful data. *128GB and 32 cores* are the minimum requirement; *256GB and 64 cores* are recommended. +EGAPx requires very substantial resources to run with real data. *128GB and 32 cores* are the minimum requirement; *256GB and 64 cores* are recommended. -There is a special test minimal example that can be run in 6GB with 4 cores. +A special minimal example that can be run in 6GB with 4 cores is provided as a yaml configuration and is used for the tool test. -In this implementation, the user can supply a yaml configuration file as initial proof of concept. +In this implementation, the user must supply a yaml configuration file as initial proof of concept. +History inputs and even a yaml editor might be provided in future. The NF workflow to tool model tested here may be applicable to other NF workflows that take a single configuration yaml. +.. class:: warningmark + +The computational resource cost of typing the wrong SRA identifiers into a tool form is potentially enormous with this tool! + Sample yaml configurations ===========================