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busco: add tar requirement #2715

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bernt-matthias
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From the logs there remains the error:

[makeblastdb]	/usr/local/bin/makeblastdb: error while loading shared libraries: libbz2.so.1

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)

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[makeblastdb]	/usr/local/bin/makeblastdb: error while loading shared libraries: libbz2.so.1

busco pins blast to < 2.4, which doesn't seem to ship bzip2 as a dependency --- but bzip2 is listed in https://github.com/bioconda/bioconda-recipes/blob/master/recipes/blast/2.2.21/meta.yaml, which is pretty weird.

tools/busco/busco.xml Outdated Show resolved Hide resolved
tools/busco/busco.xml Outdated Show resolved Hide resolved
@@ -1,12 +1,13 @@
<tool id="busco" name="Busco" version="@TOOL_VERSION@+galaxy1">
<tool id="busco" name="Busco" version="@TOOL_VERSION@+galaxy2">
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Can you also add a profile="18.01" ... the tool doesn't set detect_errors="exit_code" and we'd get this plus isolated home etc., for free.

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<tool id="busco" name="Busco" version="@TOOL_VERSION@+galaxy2">
<tool id="busco" name="Busco" version="@TOOL_VERSION@+galaxy2" profile="18.01">

bernt-matthias and others added 2 commits December 1, 2019 20:12
Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
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busco pins blast to < 2.4, which doesn't seem to ship bzip2 as a dependency --- but bzip2 is listed in https://github.com/bioconda/bioconda-recipes/blob/master/recipes/blast/2.2.21/meta.yaml, which is pretty weird.

seems that the build number was not bumped after the bzip2 requirement was added.

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mvdbeek commented Dec 1, 2019

I think it's actually 2.2.31 that gets installed, whose last known build looked like this: https://github.com/bioconda/bioconda-recipes/blob/de1a2caef2b4fa26f37e96ddbd404156a5ae2e60/recipes/blast/meta.yaml

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This seems related: bioconda/bioconda-recipes#15459

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now that bioconda/bioconda-recipes#19016 is merged we could try this one again. seems stuck anyway

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mvdbeek commented Dec 4, 2019

It passed here, the status just didn't update
It nows also passed in biocontainers:

All 5 test(s) executed passed.
busco[0]: passed
busco[1]: passed
busco[2]: passed
busco[3]: passed
busco[4]: passed

@mvdbeek mvdbeek merged commit 7686398 into galaxyproject:master Dec 4, 2019
@bernt-matthias bernt-matthias deleted the topic/busco-container-fix branch March 8, 2020 10:37
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2 participants