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Groot new tool and data manager #6043

Merged
merged 54 commits into from
Oct 17, 2024
Merged

Groot new tool and data manager #6043

merged 54 commits into from
Oct 17, 2024

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hugolefeuvre
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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)

@hugolefeuvre @bebatut
Update data_managers/data_manager_groot_database_downloader/data_mana…
582125b 
…ger/data_manager_groot_database_downloader.xml


Add requirement : python 3.12

Co-authored-by: Bérénice Batut <[email protected]>
@hugolefeuvre @bebatut
Update data_managers/data_manager_groot_database_downloader/data_mana…
58db407 
…ger/data_manager_groot_database_downloader.xml


Add ca-certificates in requirement

Co-authored-by: Bérénice Batut <[email protected]>
@hugolefeuvre @bernt-matthias
Change database path
81a1e0f 
Co-authored-by: M Bernt <[email protected]>
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hugolefeuvre commented Oct 16, 2024 •
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PR ready to be merged, I tried to condense the DM but when I pass only with a DM in xml, the test passes in local but not on git, error:

downloading the pre-clustered arg-annot database...
could not download the tarball
Get "https://github.com/will-rowe/groot/raw/master/db/clustered-ARG-databases/1.1/arg-annot.90.tar": tls: failed to verify certificate: x509: certificate signed by unknown authority

So I went back to a DM with a python file, this version works in local and on git.

@bernt-matthias
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For fixing the certificate error you need the line if [ -f '/usr/local/ssl/cacert.pem' ] ; then export SSL_CERT_FILE='/usr/local/ssl/cacert.pem' ; fi && in the command and the requirement <requirement type="package" version="2024.6.2">ca-certificates</requirement>. Then the nun-python version should work...

@hugolefeuvre
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For fixing the certificate error you need the line if [ -f '/usr/local/ssl/cacert.pem' ] ; then export SSL_CERT_FILE='/usr/local/ssl/cacert.pem' ; fi && in the command and the requirement <requirement type="package" version="2024.6.2">ca-certificates</requirement>. Then the nun-python version should work...

Indeed...I just had to not delete the line in the command part when I changed from the python version to the non-python version... Thank you

bebatut
bebatut reviewed Oct 17, 2024
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Few minor suggestions. But looks good otherwise. Thanks a lot @hugolefeuvre!

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hugolefeuvre and others added 4 commits October 17, 2024 13:47
@hugolefeuvre @bebatut
Modify DB label
a644a09 
Co-authored-by: Bérénice Batut <[email protected]>
@hugolefeuvre @bebatut
Delete default
696ea8d 
Co-authored-by: Bérénice Batut <[email protected]>
@hugolefeuvre @bebatut
Add CDATA in help part
4d5080e 
Co-authored-by: Bérénice Batut <[email protected]>
@hugolefeuvre @bebatut
Cote for log option
91702dc 
Co-authored-by: Bérénice Batut <[email protected]>
bebatut
bebatut approved these changes Oct 17, 2024
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Looks great for me. Thanks a lot @hugolefeuvre!!!

@bebatut bebatut merged commit d98a907 into galaxyproject:main Oct 17, 2024
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@hugolefeuvre hugolefeuvre deleted the groot branch October 17, 2024 14:08
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mvdbeek commented Oct 17, 2024

Attention: deployment failure!

https://github.com/galaxyproject/tools-iuc/actions/runs/11386661801

@bebatut bebatut mentioned this pull request Oct 17, 2024
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mvdbeek commented Oct 17, 2024

Attention: deployment failure!

https://github.com/galaxyproject/tools-iuc/actions/runs/11386661801

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bebatut commented Oct 17, 2024

The deployment issue (for the DM) has been fixed in #6464
The data manager has been correctly deployed, but not the tool suite. How can I force the deployment of the suite?

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You can open a PR introducing any change in on of the tools of the suite.

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