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Transfer tools from ASaiM repository #1248

Merged
merged 9 commits into from
Oct 19, 2022
Merged

Transfer tools from ASaiM repository #1248

merged 9 commits into from
Oct 19, 2022

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gallardoalba
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@gallardoalba gallardoalba commented Oct 14, 2022 •
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Only the tools which are currently installed have been moved. Related to ASaiM/galaxytools#47

@gallardoalba gallardoalba mentioned this pull request Oct 14, 2022
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@bebatut
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bebatut commented Oct 14, 2022

Thanks so much @gallardoalba!!!

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gallardoalba commented Oct 18, 2022 •
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I'm trying to fix the problem linked to dirname, but I think it is related to incompatibilities of group_humann2_uniref_abundances_to_go with Python3; could you have a look in order to confirm that @bebatut?

bebatut
bebatut reviewed Oct 19, 2022
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I gave admin access to @bgruening to the ToolShed repository. Then the changes will create a a new version, not a new tool

tools/combine_metaphlan2_humann2/.shed.yml Outdated Show resolved Hide resolved
tools/format_cd_hit_output/.shed.yml Outdated Show resolved Hide resolved
tools/compare_humann2_output/.shed.yml Outdated Show resolved Hide resolved
tools/format_metaphlan2_output/.shed.yml Outdated Show resolved Hide resolved
@bgruening
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Let's see if this works. Can someone check if those tools are on the auto-install list on EU .. if so the update should happen automtaically over the weekend.

@bgruening bgruening merged commit eea4607 into bgruening:master Oct 19, 2022
@gallardoalba
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Asaim tools are not in the auto-install list on EU, so I guess I need to include them in the bgruening.yaml file.

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Yes, that would be nice.

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bebatut commented Oct 19, 2022

Thanks @gallardoalba for the work there

@bebatut bebatut mentioned this pull request Jan 10, 2023
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@bernt-matthias
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Note, this has not been deployed: https://github.com/bgruening/galaxytools/actions/runs/3282394110

Since humann2 and metaphlan2 have been deprecated at IUC (in favor of humann and methaphlan in version 3) I was wondering if we deprecate these tools as well. If they still work with version 3 outputs we could/should keep them (but maybe change the name)

bernt-matthias added a commit to bernt-matthias/galaxytools that referenced this pull request Jan 17, 2025
@bernt-matthias
tranfer group_humann2 tool
09a093b 
finishes bgruening#1248
in order to ASaiM/galaxytools#49
@bernt-matthias bernt-matthias mentioned this pull request Jan 17, 2025
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@bgruening bgruening bgruening approved these changes

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@gallardoalba @bebatut @bgruening @bernt-matthias