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Update ABySS to 2.0.1 (Conda-only) #984

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Oct 12, 2016
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nsoranzo
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@nsoranzo nsoranzo commented Oct 7, 2016

Add test for scaffolding with long sequences.

Add test for scaffolding with long sequences.
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nsoranzo commented Oct 7, 2016

The new test fails because instead of the latest Conda abyss package, the previous one is installed, which is missing the bwa runtime requirement. This is due to the pandoc dependency of the latest abyss, which is only available in conda-forge Conda channel. It will be fixed when conda-forge is added to Galaxy/Planemo default channels.

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With galaxyproject/galaxy#3023 merged and the new Planemo 0.34.1 release (thanks @jmchilton!), all tests now pass.

<package name="abyss" version="1.9.0">
<repository name="package_abyss_1_9_0" owner="iuc"/>
</package>
</tool_dependency>
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Ahhh - XML in red - my happy place 😃.

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And more tests too!

@bgruening bgruening merged commit 586fd63 into galaxyproject:master Oct 12, 2016
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Thanks @nsoranzo !

@nsoranzo nsoranzo deleted the abyss branch October 12, 2016 17:37
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3 participants