Bioconda recipe

[amizeranschi]

Hi!

Is there any chance of getting CAT installable from Bioconda?

[ifiddes]

There is a bioconda recipe right now, that is a bit outdated, but it won't install every dependency. I am not sure how possible it would be to package tools like Augustus and HAL without them creating their own bioconda recipes to depend on.

The bioconda recipe that exists right now (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/comparative-annotation-toolkit/meta.yaml) should be sufficient for a transMap-only run of CAT with a separate install of HAL tools.

[amizeranschi]

Well, damn. I don't know how I missed that, but thanks for mentioning it. The package is indeed a bit old, but still worth checking out.

I managed to install CAT, as well as Cactus and Augustus, from bioconda. It took a good while to solve dependencies, but it went through eventually.

conda install -c conda-forge -c bioconda cactus augustus comparative-annotation-toolkit

Cactus also provides HAL.

Any chance we'll see more updates of the Bioconda recipe?

[ifiddes]

I have included language in the readme for to do a conda install by hand; I will need to figure out how to update the recipe.

However, as I noted in the readme, it is incomplete. Particularly, the version of Augustus that bioconda compiles lacks the appropriate flags to run Comparative Augustus.

[amizeranschi]

Alright, thanks for looking into this.

In the past I was able to get HAL from Bioconda by installing cactus. The version available there is quite old, but could there be a chance that this would work for CAT?

Note: the latest version of Toil (v4.1.0) is available from Bioconda: https://anaconda.org/bioconda/toil.

[ifiddes]

I am hoping to get HAL by using the new static build of cactus. I am working on a PR to try and get this to work.

https://github.com/bioconda/bioconda-recipes/pull/22626

no luck yet