[Bioperl-l] New distribution Bio-Tools-Phylo-PAML

[Fields, Christopher J]

Yep, that’s what Carnë set up: https://github.com/bioperl/Bio-Tools-Phylo-PAML

Carnë, can you go ahead and merge the commits removing these?  I can work on a version bump, and at least get a new 1.7.x point release out.

Chris

On Sep 8, 2017, at 11:45 AM, Jason Stajich <jason.stajich at ucr.edu<mailto:jason.stajich at ucr.edu>> wrote:

Prob package the Run and parser code in same distr as well I think?

Jason

On Fri, Sep 8, 2017 at 9:44 AM Jason Stajich <jason.stajich at ucr.edu<mailto:jason.stajich at ucr.edu>> wrote:
Absolutely. A separate package here makes
Complete sense and wouid hopefully make it easier to fix and update as needed. Is anyone actively willing to maintain format chasing of PAML?


On Fri, Sep 8, 2017 at 8:32 AM Fields, Christopher J <cjfields at illinois.edu<mailto:cjfields at illinois.edu>> wrote:
I personally think splitting these out into a separate PAML-specific distribution is a great idea, variations with PAML has always been hard to keep up with.  I’ll have a look at the documentation as well, if there is a way to do this for each Bio::Tools application it paves the way for combining the wrappers and parsers into separate distributions if needed.

Jason, you’re listed as key contributor for bioperl PAML development, any thoughts?

Chris

> On Sep 7, 2017, at 2:12 PM, Carnë Draug <carandraug+dev at gmail.com<mailto:carandraug%2Bdev at gmail.com>> wrote:
>
> Hi
>
> I have been preparing a new distribution for Bio::Tools::Phylo::PAML
> and related modules [1] which I would like to make a release of.
>
> To avoid clashes with existing installations, I would like to have a
> new release of bioperl-live and bioperl-run soon.  Is this possible?
> I already have commits ready for bioperl-live and bioperl-run that
> will remove the files.
>
> On a related topic, I updated the instructions on how to prepare a new
> perl distribution from a subset of modules [2] and made a new release
> of the bioperl distzilla plugin bundle [3] (will take a few hours
> before it is indexed in metacpan).
>
> Carnë
>
> [1] https://github.com/bioperl/Bio-Tools-Phylo-PAML<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bioperl_Bio-2DTools-2DPhylo-2DPAML&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=FMzJFCTUTiFNP0CYUtJrtcCUwSWZf9GRIDfyRd7KR30&s=n2vZ4HT2Fz0aOhSgB-M6_6imHSs7hpN_VZ_7nR5kUek&e=>
> [2] http://bioperl.org/howtos/split-new-distribution.html<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioperl.org_howtos_split-2Dnew-2Ddistribution.html&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=FMzJFCTUTiFNP0CYUtJrtcCUwSWZf9GRIDfyRd7KR30&s=dobD8z9YEhpdu1ToasbnMhLFpA7-FelyuS9-RL46J4c&e=>
> [3] https://metacpan.org/pod/Dist::Zilla::PluginBundle::BioPerl<https://urldefense.proofpoint.com/v2/url?u=https-3A__metacpan.org_pod_Dist-3A-3AZilla-3A-3APluginBundle-3A-3ABioPerl&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=FMzJFCTUTiFNP0CYUtJrtcCUwSWZf9GRIDfyRd7KR30&s=tU-y3qglEAMExRrf5wVvK5qgO3zevwpYJ9U5IemfQsg&e=>

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