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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.
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change Dockerfile #10

Closed maxemil closed 7 years ago

maxemil commented 7 years ago

Hej, I was trying to use the docker image, but there are still several issues that i think are unnecessary. I made some changes to the file, maybe you could have a look at them and include them if you think they are correct.

  1. When I try to build the image, I am getting a lock error from apt-get clean. However, when I change the order to first call apt-get update everything builds smoothly.

  2. When runnig the image with the -w $PWD option, It does not find the launcher script. I suggest simply linking the ALE binaries to /usr/local/bin. the usage does not change at all, it is easier to follow the Dockerfile and it works when mounting any volume to the image.

cheers, max emil

Boussau commented 7 years ago

Thanks very much Max Emil, this is cleaner and simpler!

Bastien

On Sun, Jun 25, 2017 at 11:52 AM, Max Emil Schön notifications@github.com wrote:

Hej, I was trying to use the docker image, but there are still several issues that i think are unnecessary. I made some changes to the file, maybe you could have a look at them and include them if you think they are correct.

1.

When I try to build the image, I am getting a lock error from apt-get clean. However, when I change the order to first call apt-get update everything builds smoothly. 2.

When runnig the image with the -w $PWD option, It does not find the launcher script. I suggest simply linking the ALE binaries to /usr/local/bin. the usage does not change at all, it is easier to follow the Dockerfile and it works when mounting any volume to the image.

cheers, max emil

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

https://github.com/ssolo/ALE/pull/10 Commit Summary

File Changes

Patch Links:

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-- -- 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