kgaultonlab/t1d-grs-analysis-r3-xgboost
Calculate genetic risk scores using an XGBoost mode
3.1K
kgaultonlab/t1d-grs-analysis-r3-xgboost repository overview
T1DGRS
Overview
This project provides a Docker image that can be pulled from Docker Hub and run locally. The Docker image contains all necessary dependencies and code to get started quickly.
Prerequisites
- Docker installed on your local machine. You can download Docker from here.
Getting Started
Pulling the Docker Image
To pull the latest Docker image from Docker Hub, use the following command:
docker pull kgaultonlab/t1d-grs-analysis-r3-xgboost:latest
Running the Docker Container
To run the Docker container with the necessary volume mappings, use the following command (this can be run as a bash script):
#!/bin/bash
# Run the Docker container
docker run --name my_temp_container \
-v /path/to/your/output.vcf:/data/output.vcf \
-v /path/to/your/T1GRS_allele_order.txt:/data/T1GRS_allele_order.txt \
-v /path/to/your/ALL5_199_TOPMED_SUSIE_HLA_T1D_signals_updateID_r3.vcf.alleles:/data/ALL5_199_TOPMED_SUSIE_HLA_T1D_signals_updateID_r3.vcf.alleles \
-v /path/to/your/ALL5_199_TOPMED_SUSIE_HLA_T1D_signals_updateID.vcf.alleles:/data/ALL5_199_TOPMED_SUSIE_HLA_T1D_signals_updateID.vcf.alleles \
-v /path/to/your/ALL_NoPCs_Final.ubj:/data/ALL_NoPCs_Final.ubj \
-v /path/to/your/NOHLA_NoPCs_Final.ubj:/data/NOHLA_NoPCs_Final.ubj \
-v /path/to/your/HLA_ONLY_NoPCs_Final.ubj:/data/HLA_ONLY_NoPCs_Final.ubj \
-v /path/to/your/ALL_columns.txt:/data/ALL_columns.txt \
-v /path/to/your/HLA_columns.txt:/data/HLA_columns.txt \
-v /path/to/your/nonHLA_columns.txt:/data/nonHLA_columns.txt \
-v /path/to/your/T1GRS_total_percentile_risk.txt:/data/T1GRS_total_percentile_risk.txt \
-v /path/to/your/T1GRS_MHC_percentile_risk.txt:/data/T1GRS_MHC_percentile_risk.txt \
-v /path/to/your/T1GRS_nonMHC_percentile_risk.txt:/data/T1GRS_nonMHC_percentile_risk.txt \
your-dockerhub-username/your-repo:latest \
--vcf_path /data/output.vcf --r3_variants_path /data/T1GRS_allele_order.txt --r2_snps_path /data/ALL5_199_TOPMED_SUSIE_HLA_T1D_signals_updateID_r3.vcf.alleles --allele_order_path /data/ALL5_199_TOPMED_SUSIE_HLA_T1D_signals_updateID.vcf.alleles --xgb_all_model_path /data/ALL_NoPCs_Final.ubj --xgb_nohla_model_path /data/NOHLA_NoPCs_Final.ubj --xgb_hlaonly_model_path /data/HLA_ONLY_NoPCs_Final.ubj --all_columns_path /data/ALL_columns.txt --hla_columns_path /data/HLA_columns.txt --nonhla_columns_path /data/nonHLA_columns.txt --total_percentiles_path /data/T1GRS_total_percentile_risk.txt --mhc_percentiles_path /data/T1GRS_MHC_percentile_risk.txt --nonmhc_percentiles_path /data/T1GRS_nonMHC_percentile_risk.txt --output_path /data/T1GRS_probabilities_r3.csv
# Copy the output file from the container to the host directory
docker cp my_temp_container:/data/T1GRS_probabilities_r3.csv /path/to/your/output/T1GRS_probabilities_r3.csv
Replace the paths in the -v options with your actual paths where the files are located on your host machine.
Stopping and Removing the Container
To stop the running container, use:
docker stop my_temp_container
To remove the container, use:
docker rm my_temp_container
Checking Container Logs
If you need to check the logs of the running container, use:
docker logs my_temp_container
Updating the Docker Image
To update the Docker image to the latest version, pull the latest image from Docker Hub:
docker pull your-dockerhub-username/your-repo:latest
Then, stop and remove the old container, and run the new image:
docker stop my_temp_container
docker rm my_temp_container
docker run -d --name my_temp_container your-dockerhub-username/your-repo:latest
License
See the license document for information on licensing
Contact
If you have any questions, feel free to open an issue.
Tag summary
Content type
Image
Digest
sha256:db6a00a75…
Size
579.9 MB
Last updated
about 2 years ago
docker pull kgaultonlab/t1d-grs-analysis-r3-xgboost