Ross Lazarus

Does planemo 0.72.0 test ignore PLANEMO_GLOBAL_WORKSPACE? It won't accept a --directory argument either

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Using the test command in 0.72.0 and trying to force planemo to use a specific directory - not the default ~/.planemo In cli.py there's an option: ``` @click.option('--directory', default="~/.planemo", envvar="PLANEMO_GLOBAL_WORKSPACE",...

Bump hicexplorer to 3.7.3; add dbkey if missing from input bams

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1. Hicexplorer update removes pandas dependency problems with report generation 2. If inputs were generated with a history genome, they have no metadata dbkey needed for the cool output so...

Pip is warning about mismatched `scheme.headers` in some logs coming from using quay.io/biocontainers/mulled-v2-c0c9dd2959e833cf8c69ae23a9398ddb0db5c98f:5d3a99482f42f5e17ec122729f67bf7be64df9e9-0 (planemo/git/galaxyxml) Confirmed inside the container with: ``` root@7bab7f7af205:/# pip install setuptools WARNING: Value for scheme.headers does not...

Fixes for zeekctl error loading dhcp-fp.zeek; dhcp_unknown.py updated for python3; standalone kyd.py working;

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Thanks very much for creating this zeke plugin - it's exactly what I need. This PR fixes things for me, but - I have not tried this PR any other...

Add Seqrequester https://github.com/marbl/seqrequester ---- Please read the [guidelines for Bioconda recipes](https://bioconda.github.io/contributor/guidelines.html) before opening a pull request (PR). ### General instructions * If this PR adds or updates a recipe, use...

Update jbrowse2 conda to 2.12.3

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Latest release still understands our json. - Big clean up and simplification of default view track style settings. - As part of adding working bigwig controls for colour (Yay!) and...

Make bed features from nonparametric continuous extreme bigwig value regions.

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FOR CONTRIBUTOR: * [*] I have read the [CONTRIBUTING.md](https://github.com/galaxyproject/tools-iuc/blob/master/CONTRIBUTING.md) document and this tool is appropriate for the tools-iuc repo. * [*] License permits unrestricted use (educational + commercial) * [*]...

Tagged release source tarball for the bioconda recipe linter please?

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Hello @brianwalenz and @arangrhie ! After a talk Arang gave to the VGP Galaxy group, they would like to use this package for workflows, but that means creating a Conda...

Binsize is currently in a form repeat with default length of 1 and a single default value so it always appears on the command line - there is no way...

Propose two VGP workflows generating customised browsers

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Draft of two VGP workflows for review and suggestions. Basic tracks [documentation draft](https://docs.google.com/document/d/1YbQZsFC8oDJIGos5yLFbApumpK4yIz02qfwYEypDfI8) Dimers, coverage, SV [documentation draft](https://docs.google.com/document/d/1kFCpCGt7Itb3R1mXiNSigd6_mT7-8J0mjYJppliPYtQ/edit#heading=h.i99j8o3qfj7)