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Trinity 2.6.6 #1937

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merged 11 commits into from Jun 14, 2018

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@abretaud
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abretaud commented Jun 12, 2018

Here's an update from Trinity 2.4.0 to 2.6.6
Now there's a wrapper to generate super transcripts.
As things would have been too simple with just changing the @WRAPPER_VERSION@, I also add to update a few dependencies, countless test data, and update some wrappers a now trinity generates a gene map that needs to be reused by some of the scripts (replacing --trinity_mode)

abretaud added some commits Jun 8, 2018

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bgruening left a comment

Great work @abretaud! I just have two small comments :)

<option value="no">No</option>
</param>
<when value="yes">
<param format="tabular" name="gene_trans_map" argument="--gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" />

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bgruening Jun 13, 2018

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could you not just use the param and make it optional and remove the conditional?

</macros>
<expand macro="requirements"/>
<command detect_errors="aggressive"><![CDATA[
Trinity_gene_splice_modeler.py --incl_malign --trinity_fasta "$assembly"

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bgruening Jun 13, 2018

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single quotes

abretaud and others added some commits Jun 13, 2018

@bgruening bgruening merged commit 9dcdb53 into galaxyproject:master Jun 14, 2018

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bgruening commented Jun 14, 2018

Thanks @abretaud!

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lldelisle commented Jun 26, 2018

Hi,
In my private instance, the dependency is not solved. Is there a package trinity 2.6.6 to download?
Many thanks,

Lucille

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abretaud commented Jun 27, 2018

@lldelisle there's a conda package for this version of trinity (https://anaconda.org/bioconda/trinity)
If your galaxy is configured to use conda for dependency resolution, it should install automatically
We no longer maintain old-style tool_dependency.xml for trinity

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