oakvar: set config

Take this config file:

.oakvar/conf/system.yml

publish_url: https://store.oakvar.com
store_url: https://store.oakvar.com
base_modules:
- csv-converter
- maf-converter
- vcf-converter
- textreporter
- excelreporter
- vcfreporter
- stdoutreporter
- tagsampler
- vcfinfo
- gencode
- wgbase
- wghg19
- wgncrna
- wglollipop
- wgndex
- wgcircossummary
- wgcodingvsnoncodingsummary
- wggosummary
- wgsosamplesummary
- wgsosummary
- wgnote
- wgvcfinfo
- hg38wgs
- wgrankscore
num_input_line_warning_cutoff: 25000
gui_input_size_limit: 500
max_num_concurrent_jobs: 4
max_num_concurrent_annotators_per_job: 1
gui_port: 8080
gui_port_ssl: 8444
server_default_username: default
result_viewer_num_var_limit_for_gene_summary: 100000
result_viewer_num_var_limit_for_summary_widget: 100000
report_filter_max_num_cache_per_user: 20
sys_conf_path: /home/admin/.oakvar/conf/system.yml
root_dir: /opt/oakvar-root
conf_dir: /opt/oakvar-root/conf/conf
liftover_dir: /opt/oakvar-root/conf/conf/liftover
modules_dir: /mnt/ov-modules
jobs_dir: /opt/oakvar-root/jobs
log_dir: /opt/oakvar-root/logs
package_dir: /opt/oakvar-longevity-env/lib/python3.11/site-packages/oakvar

the way to thing about it, perhaps. Is .

Where in the process should we overwrite the config file that oakvar generates automatically when running ov system setup -f config.yaml It still creates another config file in the users $HOME directory which is super annoying!!

We basically need to overwrite it AND also automate it, but at least we know wtf is going on.