General utility scripts for Quetzal projects
Project description
quetzal-CRUMBS
General utility scripts for Quetzal projects
Updating the package
From https://circleci.com/blog/publishing-a-python-package/ :
- Create a
feature
branch, make updates to it. - Test the feature
- Bump the version in
setup.py
- Bump the version of the
whl
file in.circleci/config.yml
- Update the ChangeLog
- Push to GitHub
When you have a successful build on https://app.circleci.com/pipelines/github/Becheler/quetzal-CRUMBS:
- create a Pull Request (PR) to the develop branch
- Merge the PR if it looks good.
- When that build succeeds, create a PR to the main branch, review it, and merge.
- Go get a beer and bless this new version with some luuuv.
# Usage
To visualize the parameter space:
What parameters lead to simulation that failed?
ids=$(python3 -m crumbs.get_simulations_ID "output.db", "quetzal_EGG_1", failed=True)
What parameters lead to successful simulations?
ids=$(python3 -m crumbs.get_simulations_ID "output.db", "quetzal_EGG_1", failed=False)
for i in ids do s=$(python3 -m crumbs.sample "uniform_real" 0.00025 0.0000025)
python3 -m crumbs.simulate_sequences
--database "output.db"
--table "quetzal_EGG_1"
--rowid $i
--sequence_size 1041
--scale_tree $s
--output "pods/phylip/EGG1_pod_"$i".phyl"
python3 -m crumbs.phylip2arlequin
--input "pods/phylip/EGG1_pod_"$i".phyl"
--imap "imap.txt"
--output "pods/arlequin/EGG1_pod_"$i".arp"
if [ $i -eq 1 ]; then ./arlsumstat3522_64bit "pods/arlequin/EGG1_pod_"$i".arp" outSS 0 1 run_silent else ./arlsumstat3522_64bit "pods/arlequin/EGG1_pod_"$i".arp" outSS 1 0 run_silent fi rm "pods/arlequin/EGG1_pod_"$i".res" -r
## Dependencies
### GDAL/OGR for Python:
- [Ubuntu installation](https://mothergeo-py.readthedocs.io/en/latest/development/how-to/gdal-ubuntu-pkg.html)
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