Replace treetime submodule by treetime from conda - Githubissues

neherlab / pan-genome-analysis

Processing pipeline for pan-genome visulization and exploration

http://pangenome.de

GNU General Public License v3.0

134 stars 38 forks source link

Replace treetime submodule by treetime from conda #4

Closed bebatut closed 6 years ago

bebatut commented 6 years ago

Hi,

This PR replaces the submodule for treetime to use the treetime installed with conda:

Remove the submodule
Add treetime in conda environment
Fix import of treetime

I ran the tests to check.

Bérénice

bebatut commented 6 years ago

@wdingx What do you think about this Pull Request? It would be helpful to make sure the Bioconda recipe will work correctly

wdingx commented 6 years ago

Thanks for this PR. I have already talked about it with Richard @rneher. He will take some time to consider it.

rneher commented 6 years ago

sorry for being slow here. I think we can remove treetime as a submodule along the lines @bebatut suggests. At the time, treetime was very much in flux and a submodule ensured stability. @wdingx , could you test and merge this?

wdingx commented 6 years ago

@bebatut OK. I am currently on vacation and will work on it in the first week of March. Thanks.

bebatut commented 6 years ago

@wdingx Did you have the time to work on this pull request? We have a project using panx waiting for this fix 😄

wdingx commented 6 years ago

@bebatut Yes. I tested this PR and it has passed the panX analysis pipeline. I am asking @rneher to double-check it. If everything is fine, we will soon merge it. Thanks.

wdingx commented 6 years ago

@bebatut I pushed a new branch. Please first use that for your project and let me know if you have any questions. https://github.com/neherlab/pan-genome-analysis/tree/bebatut-remove_treetime

bebatut commented 6 years ago

@wdingx Thanks a lot! Is it possible to get a release such that I can update the conda recipe? Thanks a lot!!!!

wdingx commented 6 years ago

Thanks. @bebatut v1.6.0 released