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update ViennaRNA - #1851

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bgruening wants to merge 2 commits into
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viennarna
Open

update ViennaRNA#1851
bgruening wants to merge 2 commits into
masterfrom
viennarna

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@bgruening

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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)

There are two labels that allow to ignore specific (false positive) tool linter errors:

  • skip-version-check: Use it if only a subset of the tools has been updated in a suite.
  • skip-url-check: Use it if github CI sees 403 errors, but the URLs work.

@bgruening

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The kinwalker binary in quay.io/biocontainers/viennarna:2.7.2--py313pl5321h1f5d440_1 segfaults on any sequence input.

No idea if this is a bug in the conda recipe?

<expand macro="requirements"/>
<expand macro="version_command"/>
<command detect_errors="aggressive"><![CDATA[
ln -s '$input' ./input.{$input.ext} &&

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@pavanvidem this is just a guess. I hope this helps with https://github.com/usegalaxy-eu/issues/issues/978

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Its not clear if its working and if we need this for all tools here.

@pavanvidem

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latest conda version that works v2.7.0. For now, keeping it to v2.7.0. I tried to fix the recipe, but no luck so far. When I compiled v2.7.2 independently of conda, it worked, though.

@bgruening

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Good for me, if the tests are passing :)

@bgruening bgruening changed the title [WIP] update ViennaRNA update ViennaRNA Aug 30, 2026
<description>Simulate cotranscriptional folding of RNAs</description>
<macros>
<token name="@EXECUTABLE@">kinwalker</token>
<token name="@TOOL_VERSION@">2.6.4</token>

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@pavanvidem I downgraded kinwalker here. Its not working for me in 2.7.

@RaumZeit is this known? We get corrupted files or segfaults using the conda package/conatainer in version 2.7.x

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2 participants