search

ssolo / ALE

Amalgamated likelihood estimation (ALE) is a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (cf. http://arxiv.org/abs/1211.4606 ), which allows for the duplication, transfer and loss of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees.
44 stars 15 forks source link

update travis configuration and clean up merge artifact #11

Closed maxemil closed 7 years ago

maxemil commented 7 years ago

Hej, I just saw that you pushed some fixes for the fractionMissing option. Nice! However, there was some problem with the git merge artifact which was still in the code. I tried to clean that up (but not sure i picked the right lines, i picked from HEAD). Also i liked the idea of adding CI with travis, so i rewrote the travis config file and it now works by trying to build and execute the docker image. MAube it would be good though to check for all the binaries in the ALEsuite.

cheers, maxemil

Boussau commented 7 years ago

Thanks maxemil! We are just starting with Travis, actually we have not even linked Travis to the repo yet, but your changes seem great! Regarding simulation.cpp, sorry, I had not seen that there had been a merge issue. It should be OK now. Thanks again!

Bastien

On Wed, Jun 28, 2017 at 9:57 AM, Max Emil Schön notifications@github.com wrote:

Hej, I just saw that you pushed some fixes for the fractionMissing option. Nice! However, there was some problem with the git merge artifact which was still in the code. I tried to clean that up (but not sure i picked the right lines, i picked from HEAD). Also i liked the idea of adding CI with travis, so i rewrote the travis config file and it now works by trying to build and execute the docker image. MAube it would be good though to check for all the binaries in the ALEsuite.

cheers, maxemil

You can view, comment on, or merge this pull request online at:

https://github.com/ssolo/ALE/pull/11 Commit Summary

  • add docker build to travis, try fixing simulation
  • try fixing travis and the docker building
  • test if binaries are available in docker image
  • undo changes to dockerfile

File Changes

Patch Links:

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ssolo/ALE/pull/11, or mute the thread https://github.com/notifications/unsubscribe-auth/ABcp-JjRjLyLtLJtl9qD-4cL43DvmIbuks5sIgeHgaJpZM4OHnft .

-- -- Bastien Boussau, PhD

Chercheur CNRS Equipe Bioinformatique Phylogénie et Génomique Evolutive LBBE, UMR5558, Université de Lyon Villeurbanne, France Lab page http://lbbe.univ-lyon1.fr/-Boussau-Bastien-.html?lang=en