https://github.com/kaczmarj/variational_lsrc
https://github.com/kaczmarj/variational_lsrc
Last synced: about 2 months ago
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- Host: GitHub
- URL: https://github.com/kaczmarj/variational_lsrc
- Owner: kaczmarj
- Created: 2018-06-07T15:56:27.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2018-06-07T19:15:15.000Z (almost 7 years ago)
- Last Synced: 2025-02-10T02:33:31.609Z (4 months ago)
- Language: Python
- Size: 26.4 KB
- Stars: 0
- Watchers: 3
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# variational_lsrc
docker url:
https://hub.docker.com/r/ysa6/genus/
command to build using singularity:
```
singularity build genus_img.sqsh docker://ysa6/genus:latest
```
command to run the container
```
singularity shell --bind /storage:/storage genus_img.sqsh
```
General logic of execution:
1. `gtoi.py`
* a) `write_varbvs` function creates directory structure and writes a bash file that calls the `gtoi_template.r` file when inside the singularity image
* b) `run_sing` function writes batch files for slurm that execute a singularity image with all dependencies and environmental variables to run the analysis.
* example command
```
python gtoi.py -dp /storage/gablab001/data/genus/GIT/genus/bayes/data_sets/files_for_edward/brain_snp_covars_meancentered_scaled.h5 \
-sn /storage/gablab001/data/genus/GIT/genus/bayes/data_sets/files_for_edward/dev_for_container/bf_out \
-nr 170 \
-ip /storage/gablab001/data/genus/GIT/genus/genus_img.sqsh \
-bp /storage:/storage \
-cn I_cols
```