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comparison egapx_runner.xml @ 6:a7304162d737 draft

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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
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5:6effccc966d0 6:a7304162d737
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>
20 <option value="docker">Docker requires at least 128GB ram and 32 cores. 256GB and 64 cores recommended</option> 20 <option value="docker">Docker: requires at least 128GB ram and 32 cores. 256GB and 64 cores recommended</option>
21 </param> 21 </param>
22 </inputs> 22 </inputs>
23 <outputs> 23 <outputs>
24 <collection name="egapx_out" type="list" label="Outputs from egapx"> 24 <collection name="egapx_out" type="list" label="Outputs from egapx">
25 <discover_datasets pattern="__name_and_ext__" directory="egapx_out" visible="false"/> 25 <discover_datasets pattern="__name_and_ext__" directory="egapx_out" visible="false"/>
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 .. class:: warningmark
45
44 **Proof of concept: a quick hack to run a NF workflow inside a specialised Galaxy tool wrapper** 46 **Proof of concept: a quick hack to run a NF workflow inside a specialised Galaxy tool wrapper**
45 47
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. 48 EGAPx is a big, complicated Nextflow workflow, challenging and costly to re-implement **properly**, requiring dozens of new tools and replicating a lot of
49 complicated *groovy* workflow logic.
47 50
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*. 51 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*.
49 52
50 This wrapper is designed to allow measuring how *inefficient* it is in terms of computing resource utilisation, in comparison to the developer effort 53 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. 54 required to convert Nextflow DDL into tools and WF logic. Balancing these competing requirements is a fundamental Galaxy challenge.
52 55
53 56
54 EGAPx requires huge resources to run with useful data. *128GB and 32 cores* are the minimum requirement; *256GB and 64 cores* are recommended. 57 EGAPx requires very substantial resources to run with real data. *128GB and 32 cores* are the minimum requirement; *256GB and 64 cores* are recommended.
55 58
56 There is a special test minimal example that can be run in 6GB with 4 cores. 59 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.
57 60
58 In this implementation, the user can supply a yaml configuration file as initial proof of concept. 61 In this implementation, the user must supply a yaml configuration file as initial proof of concept.
62 History inputs and even a yaml editor might be provided in future.
59 63
60 The NF workflow to tool model tested here may be applicable to other NF workflows that take a single configuration yaml. 64 The NF workflow to tool model tested here may be applicable to other NF workflows that take a single configuration yaml.
65
66 .. class:: warningmark
67
68 The computational resource cost of typing the wrong SRA identifiers into a tool form is potentially enormous with this tool!
61 69
62 70
63 Sample yaml configurations 71 Sample yaml configurations
64 =========================== 72 ===========================
65 73