search

rkimoakbioinformatics / oakvar

Genomic variant analysis platform
Other
32 stars 8 forks source link

No cravat-system.yml file and packagedir is not defined errors during installation #1

Closed Alex-Karmazin closed 2 years ago

Alex-Karmazin commented 2 years ago

I install oakvar on linux (Ubuntu 20.04.3 LTS) under micromamba with command "pip install oakvar" then I use command "oc module installbase" and get error there is no file cravat-system.yml. I found cravat-system.template.yml and renamed it. Then "oc module installbase" start getting different error. """ Traceback (most recent call last): File "/home/alex/micromamba/envs/opencravat-longevity/bin/oc", line 5, in from oakvar.main import main File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/site-packages/oakvar/init.py", line 52, in from . import main as cli File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/site-packages/oakvar/main.py", line 5, in from .cli_gui import get_parser_fn_gui File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/site-packages/oakvar/cli_gui.py", line 9, in sysconf = get_system_conf() File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/site-packages/oakvar/admin_util.py", line 939, in get_system_conf conf[modules_dir_key] = get_default_modules_dir() File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/site-packages/oakvar/admin_util.py", line 2005, in get_default_modules_dir return pathjoin(get_ov_root_dir(), modules_dir_name) File "/home/alex/micromamba/envs/opencravat-longevity/lib/python3.9/site-packages/oakvar/admin_util.py", line 1886, in get_ov_root_dir root_dir = packagedir NameError: name 'packagedir' is not defined """

rkimoakbioinformatics commented 2 years ago

@Alex-Karmazin I'll look into it.

rkimoakbioinformatics commented 2 years ago

@Alex-Karmazin I'm fixing the issue. While doing so, the setup process is being improved, so that ov system setup will do all the setup processes. The new version will be released shortly.

rkimoakbioinformatics commented 2 years ago

@Alex-Karmazin OakVar v2.4.2 has been released (release note at https://github.com/rkimoakbioinformatics/oakvar/releases/tag/2.4.2). Let me know if it solves the issue. Details of ov system setup will be on oakvar.readthedocs.io soon.

Alex-Karmazin commented 2 years ago

Thank you will try soon.

rkimoakbioinformatics commented 2 years ago

@Alex-Karmazin Documentation has been updated with installation and setup instructions. See https://oakvar.readthedocs.io.