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kraemer-lab / vneyard

Repository for GRAPEVNE modules
MIT License
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changed beagle==4.1_21Jan17.6cc.jar to beagle-lib=3.1.2 #29

Closed joetsui1994 closed 3 months ago

joetsui1994 commented 3 months ago

beagle==4.1_21Jan17.6cc.jar (https://anaconda.org/bioconda/beagle) is actually not the beagle library we want. Rhys did some testing and found that beagle-lib=3.1.2 (https://bioconda.github.io/recipes/beagle-lib/README.html) is the only one that works.

jsbrittain commented 3 months ago

@joetsui1994 can we add a test to confirm that this is working properly on mac and linux? (at the moment tests are passing because there are no test to run!) Following #26 , we can add a .test.sh file in the main BEAST folder with the following contents:

#!/usr/bin/env bash

rm -rf results/out
snakemake --cores 1 --use-conda

(be sure to make it executable before pushing to github)

Since there is already a sample input.xml file in the results/in folder, the module will use that with default parameters to run through.

Edit: You don't need CONDA_SUBDIR=osx-64 as that is set by default on the runners (better to leave if off for compatibility).

joetsui1994 commented 3 months ago

Moved to https://github.com/kraemer-lab/vneyard/pull/31.