pplacer 1.1.alpha19 or 1.1.alpha17 - BioConda - guppy - RaXML 8

[AjitPS]

Hi @matsen, This is a question around pplacer in bioconda, to be used in Galaxy.

We have an older tool wrapper developed for Galaxy which uses pplacer 1.1.alpha11 with RaXML 7.3.

We also have RaXML 8.0 installed in Galaxy via conda and were thinking of upgrading to the latest pplacer (1.1.alpha19). However, bioconda only has pplacer 1.1.alpha17: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/pplacer/meta.yaml

I tried installing that via bioconda but the install & v.env creation failed. Before I work on this more, I wanted to confirm that 1.1.alpha17 release supports RaXML 8 and also if it has guppy in it?

Thanks.

[AjitPS]

any thoughts on this @matsen ? thanks.

FYI @hughesdj

[matsen]

Hello @AjitPS --

All pplacer releases have guppy in them.

We stopped directly supporting RAxML output in pplacer ages ago. The modern way is to use a reference package made with http://fhcrc.github.io/taxtastic/. I don't know how the Galaxy wrapper works, but taxtastic does support RAxML 8 as far as I know.

Please close if this answers your questions.

Thanks!

[AjitPS]

Thanks @matsen, is taxtastic in bioconda then so we could use it in Galaxy via conda, to replace our RaXML Galaxy tool wrapper ?

Also, we had developed a Galaxy wrapper for pplacer 1.1.alpha11 in the past but wanted to upgrade to pplacer 1.1.alpha19 which we are using via command line. Bioconda lists pplacer 1.1.alpha17 so I tried getting it in Galaxy but the conda install fails. I'm not sure if there's an issue with the conda recipe for pplacer.

[matsen]

is taxtastic in bioconda then so we could use it in Galaxy via conda, to replace our RaXML Galaxy tool wrapper ?

I don't think so, but it's here: https://pypi.python.org/pypi/taxtastic

There may be a problem with the conda recipe, I'm not sure. alpha17 is nearly the same as alpha19.

[AjitPS]

Thanks @matsen , does the alpha17 conda recipe (https://bioconda.github.io/recipes/pplacer/README.html) work at your end ? Because conda install for alpha17 fails for me. I notice taxtastic 0.5.4 is also in BioConda so we could use raxml 8.2.4, taxtastic 0.5.4 & pplacer 1.1.alpha17 in Galaxy to replace our old usage of raxml 7 and old pplacer code.

[AjitPS]

Hi @matsen , does the alpha17 conda recipe (https://bioconda.github.io/recipes/pplacer/README.html) work for you?

[matsen]

It does install, and runs --help.

(pplacer) stoat ~ » uname -a
Linux stoat 3.13.0-45-generic #74-Ubuntu SMP Tue Jan 13 19:36:28 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux