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metaphlan v4.0.5 -> v4.0.6 #5218

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merged 5 commits into from
Mar 28, 2023
Merged

metaphlan v4.0.5 -> v4.0.6 #5218

merged 5 commits into from
Mar 28, 2023

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tuncK
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@tuncK tuncK commented Mar 28, 2023 •
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FOR CONTRIBUTOR:

  • - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • - License permits unrestricted use (educational + commercial)
  • - This PR adds a new tool or tool collection
  • - This PR updates an existing tool or tool collection
  • - This PR does something else (explain below)

Updated metaphlan version, commented out DM test as the target file is too big to be used as a test.

bgruening
bgruening reviewed Mar 28, 2023
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.../data_manager_metaphlan_database_downloader/data_manager/data_manager_metaphlan_download.xml
@@ -26,6 +26,7 @@ python '$__tool_directory__/data_manager_metaphlan_download.py'
<data name="out_file" format="data_manager_json" label="${tool.name}"/>
</outputs>
<tests>
<!--
<test expect_num_outputs="1">
<param name="index" value="mpa_vOct22_CHOCOPhlAnSGB_202212"/>
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can we download a smaller dataset?

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None available: http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/bowtie2_indexes/

Unless we go the VW-way and make it download via "if toy DB, wget ... else call python"

@tuncK tuncK mentioned this pull request Mar 28, 2023
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bernt-matthias
bernt-matthias approved these changes Mar 28, 2023
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Hi @tuncK and @bgruening

Fine from my side. CI considers the tool now .. but at the same time all tests have been commented.

Guess there is nothing else that we can do, or?

What is the limiting factor in testing: time or disk space?

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As far as I understood its a space limitation. I also have no better idea. Please feel free to merge.

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As far as I understood its a space limitation. I also have no better idea. Please feel free to merge.

yep to large. 2GB .. needing ~200min

@bernt-matthias bernt-matthias merged commit 57df6e8 into galaxyproject:main Mar 28, 2023
paulzierep pushed a commit to paulzierep/tools-iuc that referenced this pull request Apr 18, 2023
@tuncK @bernt-matthias @paulzierep
metaphlan v4.0.5 -> v4.0.6 (galaxyproject#5218)
7881b56 
* metaphlan v4.0.6

* Update tools/metaphlan/macros.xml

* remove metaphlan DM from skip list

* Try to enable tests

* Revert "Try to enable tests"

This reverts commit 0f1d8f8.

---------

Co-authored-by: M Bernt <[email protected]>
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@bernt-matthias bernt-matthias bernt-matthias approved these changes

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@tuncK @bgruening @bernt-matthias