Mercurial > repos > fubar > egapx_runner

comparison egapx_runner.xml @ 5:6effccc966d0 draft

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planemo upload for repository https://github.com/ncbi/egapx commit 9e59da535540cb4d5c1c412bb2b0969744dfb0b0
author fubar
date Sun, 04 Aug 2024 01:59:37 +0000
parents 6592ae57bb8b
children a7304162d737
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4:6592ae57bb8b 5:6effccc966d0
9 </requirements> 9 </requirements>
10 <version_command><![CDATA[echo "6.0.1"]]></version_command> 10 <version_command><![CDATA[echo "6.0.1"]]></version_command>
11 <command><![CDATA[mkdir -p ./egapx_config && 11 <command><![CDATA[mkdir -p ./egapx_config &&
12 #set econfigfile = $econfig + '.config' 12 #set econfigfile = $econfig + '.config'
13 cp '$__tool_directory__/ui/assets/config/executor/$econfigfile' ./egapx_config/ && 13 cp '$__tool_directory__/ui/assets/config/executor/$econfigfile' ./egapx_config/ &&
14 python '$__tool_directory__/ui/egapx.py' '$yamlconfig' -e '$econfig' -o 'egapx_out']]></command> 14 python '$__tool_directory__/ui/egapx.py' '$yamlconfig' -e '$econfig' -o 'egapx_out']]></command>
15 <inputs> 15 <inputs>
16 <param name="yamlconfig" type="data" optional="false" label="egapx configuration yaml file to execute" help="" format="yaml,txt" multiple="false"/> 16 <param name="yamlconfig" type="data" optional="false" label="egapx configuration yaml file to execute" help="" format="yaml,txt" multiple="false"/>
17 <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"> 17 <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">
18 <option value="docker_minimal">Docker_minimal supports only the minimal dust mite example yaml using 6GB and 4 cores</option> 18 <option value="docker_minimal">Docker_minimal supports only the minimal dust mite example yaml using 6GB and 4 cores</option>
19 <option value="singularity">Singularity requires at least 128GB ram and 32 cores. 256GB and 64 cores recommended</option> 19 <option value="singularity">Singularity requires at least 128GB ram and 32 cores. 256GB and 64 cores recommended</option>
39 39
40 <help><![CDATA[ 40 <help><![CDATA[
41 Galaxy tool wrapping the Eukaryotic Genome Annotation Pipeline (EGAPx) 41 Galaxy tool wrapping the Eukaryotic Genome Annotation Pipeline (EGAPx)
42 ================================================================================================= 42 =================================================================================================
43 43
44 **A very simple and crude way to run the EGAPx workflows inside Galaxy** 44 **Proof of concept: a quick hack to run a NF workflow inside a specialised Galaxy tool wrapper**
45 45
46 EGAPx requires huge resources to run with useful data. *128GB and 32 cores* are the minimum requirement; *256GB and 64 cores* are recommended. 46 EGAPx is a big, complicated Nextflow workflow, challenging and costly to re-implement **properly**, requiring dozens of new tools and complicated ``groovy`` WF logic.
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48 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*.
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50 This wrapper is designed to allow measuring how *inefficient* it is in terms of computing resource utilisation, in comparison to the developer effort
51 required to convert Nextflow DDL into tools and WF logic. Balancing these competing requirements is a fundamental Galaxy challenge.
52
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54 EGAPx requires huge resources to run with useful data. *128GB and 32 cores* are the minimum requirement; *256GB and 64 cores* are recommended.
47 55
48 There is a special test minimal example that can be run in 6GB with 4 cores. 56 There is a special test minimal example that can be run in 6GB with 4 cores.
49 57
50 In this implementation, the user can supply a yaml configuration file as initial proof of concept. 58 In this implementation, the user can supply a yaml configuration file as initial proof of concept.
51 59
52 Does not use computational resources as efficiently as converting the NF workflow components into Galaxy tools, but it is very simple to maintain until EGAPx becomes stable. It will also enable measurement of the actual loss of efficiency from the crude wrapping method. 60 The NF workflow to tool model tested here may be applicable to other NF workflows that take a single configuration yaml.
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54 62
55 Sample yaml configurations 63 Sample yaml configurations
56 =========================== 64 ===========================
57 65