Running a Treesearch

1. go to the instance dashboard
2. Launch an instance -> My AMIs -> select treesearch-ami
3. ssh into it
4. download the alignment(s) (either with aws s3 cp which requires credentials, or you scp them from your host), lets call it aln.afa and aln2.afa
5. make a tmux or screen session, whatever you're comfy with
6. call docker run --rm --mount src=${PWD},target=/data,type=bind treesearch -t 70 -d aa -p /data aln.afa aln2.afa (but modify -t 70 to your desired threads, and -d aa to nt if it's not amino acid data)
7. wait for it to finish
8. results will be under result/

Bonus: you can watch it work live with (substitute aln with the name sans postfix of your input file)

less +F result/aln/apriori/pargenes/pargenes_run/mlsearch_run/logs.txt