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Updating tools/bcftools from version 1.15.1 to 1.21 #3945

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Updating tools/bcftools from version 1.15.1 to 1.21 #3945

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planemo-autoupdate
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Hello! This is an automated update of the following tool: tools/bcftools. I created this PR because I think the tool's main dependency is out of date, i.e. there is a newer version available through conda.

Please see https://github.com/planemo-autoupdate/autoupdate for more information.

@planemo-autoupdate planemo-autoupdate changed the title Updating tools/bcftools tool version(s) Updating tools/bcftools tool to 1.14 Oct 29, 2021
@planemo-autoupdate planemo-autoupdate changed the title Updating tools/bcftools tool to 1.14 Updating tools/bcftools tool to 1.14 1.15 Feb 28, 2022
@planemo-autoupdate planemo-autoupdate changed the title Updating tools/bcftools tool to 1.14 1.15 Updating tools/bcftools tool to 1.14 1.15 1.15.1 Apr 11, 2022
@planemo-autoupdate planemo-autoupdate changed the title Updating tools/bcftools tool to 1.14 1.15 1.15.1 Updating tools/bcftools tool to 1.14 1.15 1.16 Oct 10, 2022
@planemo-autoupdate planemo-autoupdate changed the title Updating tools/bcftools tool to 1.14 1.15 1.16 Updating tools/bcftools tool to 1.14 1.15 1.17 Apr 20, 2023
@nsoranzo nsoranzo changed the title Updating tools/bcftools tool to 1.14 1.15 1.17 Updating tools/bcftools tool to 1.14 1.155.4_22Jul22.46e Oct 30, 2023
@nsoranzo nsoranzo changed the title Updating tools/bcftools tool to 1.14 1.155.4_22Jul22.46e Updating tools/bcftools tool from version 1.10 to 1.18 Oct 30, 2023
@nsoranzo nsoranzo changed the title Updating tools/bcftools tool from version 1.10 to 1.18 Updating tools/bcftools from version 1.10 to 1.18 Oct 30, 2023
@gxydevbot gxydevbot changed the title Updating tools/bcftools from version 1.10 to 1.18 Updating tools/bcftools from version 1.10 to 1.19 Feb 5, 2024
@gxydevbot gxydevbot changed the title Updating tools/bcftools from version 1.10 to 1.19 Updating tools/bcftools from version 1.10 to 1.20 Apr 22, 2024
@aghozlane
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Dear maintainers,

We are maintaining a galaxy instance at pasteur and we have users of this package. A lot of update were performed since the current version 1.15.1 and we would like that our users benefit from the last version. Could you update the package ?

Best regards,
Amine

@bernt-matthias
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Dear Amine, we need to at least fix the tests (ideally adding new arguments). Seems that we could need help with this. Could you contribute?

@aghozlane
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We have test data and some experience with bcftools. However, the Galaxy administrators will be on holiday break by the end of the week.

nsoranzo
nsoranzo reviewed Aug 23, 2024
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tools/bcftools/bcftools_call.xml
@@ -1,4 +1,4 @@
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy5" profile="@PROFILE@">
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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Suggested change
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">

tools/bcftools/bcftools_mpileup.xml
@@ -1,4 +1,4 @@
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@">
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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Suggested change
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">

@nsoranzo nsoranzo changed the title Updating tools/bcftools from version 1.10 to 1.20 Updating tools/bcftools from version 1.15.1 to 1.20 Aug 24, 2024
@nsoranzo
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nsoranzo commented Sep 2, 2024

Mmmh, it seems gxydevbot force-pushed on this branch even if it contained commits from @bgruening . Any idea @lldelisle ?

@bgruening
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here are my other changes: #6293

I'm wondering how many other branches just got overwritten.

@gxydevbot
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There are new updates, if you want to integrate them, close the PR and delete branch.

@gxydevbot gxydevbot changed the title Updating tools/bcftools from version 1.15.1 to 1.20 Updating tools/bcftools from version 1.15.1 to 1.21 Sep 23, 2024
@gxydevbot
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There are new updates, they have been integrated to the PR, check the file diff.

@gxydevbot
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There are new updates, they have been integrated to the PR, check the file diff.

@lldelisle
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Mmmh, it seems gxydevbot force-pushed on this branch even if it contained commits from @bgruening . Any idea @lldelisle ?

Really sorry, this has been fixed in planemo-autoupdate/autoupdate@41025ee
I hope there were no other damage...

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7 participants
@planemo-autoupdate @aghozlane @bernt-matthias @nsoranzo @bgruening @gxydevbot @lldelisle