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popsim-consortium / analysis2

Analysis for the second consortium paper.
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changes to reflect dadi-cli updates #80

Closed chriscrsmith closed 1 year ago

chriscrsmith commented 1 year ago

I noticed the DFE side of the pipeline was broken, so I changed some command line flags and redirected some outputs. The pipeline runs for me now.

chriscrsmith commented 1 year ago

Thanks for the edits @xin-huang. Pipeline runs fine for me

andrewkern commented 1 year ago

i went to review this PR, but ran into an issue with dadi-cli that I believe is unrelated. Here's that issue https://github.com/xin-huang/dadi-cli/issues/59

Hopefully that will be resolved quickly and we can merge this PR

andrewkern commented 1 year ago

okay that issue had to do with a dadi version problem. @chriscrsmith can you pin the version of dadi in the environment.yml file to dadi==2.2.0 and push that commit to this PR? Then we can squash and merge

chriscrsmith commented 1 year ago

whoops! I messed something up. Something weird in my commit history.

Can I please get a second set of eyes on the code before I squash?

chriscrsmith commented 1 year ago

also, I'm seeing a TON of files here: ./ext/dfe-alpha-release-2.16/data/n1_100_adv/n1_n2_t2_s_vec_dir/n1:100

are y'all getting the same?

andrewkern commented 1 year ago

chris those files should be ignored by git. check the .gitignore file

chriscrsmith commented 1 year ago

right on. They aren't trivial size. But I'm fine with it if you are!

chriscrsmith commented 1 year ago

follow up: Andy reminded me those files are used by DFEalpha so they are supposed to be there