A machine learning genetic risk score for T1D.
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This project provides a T1GRS Docker image that can be pulled from Docker Hub and run locally. The Docker image contains all necessary dependencies and test data to get started quickly.
First, pull the Docker image from Docker Hub:
docker pull kgaultonlab/t1grs:latest
Run the Docker container using the image you pulled. All necessary data is already included in the image, so you do not need to mount any external volumes. Use the following script to run the container and execute the analysis:
#!/bin/bash
# Run the Docker container
docker run --name t1grs_analysis_container kgaultonlab/t1grs:latest \
--vcf_path /data/T1GRS_test_data.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 t1grs_analysis_container:/data/T1GRS_probabilities_r3.csv /path/to/your/output/directory/T1GRS_probabilities_r3.csv
# Stop and remove the container
docker stop t1grs_analysis_container
docker rm t1grs_analysis_container
Replace /path/to/your/output/directory with the actual path where you want to save the output file on your host machine.
Copyright Notice
This software is Copyright © 2024 The Regents of the University of California. All Rights Reserved. Permission to copy, modify, and distribute this software and its documentation for educational, research, and non-profit purposes, without fee, and without a written agreement is hereby granted, provided that the above copyright notice, this paragraph, and the following three paragraphs appear in all copies. Permission to make commercial use of this software may be obtained by contacting:
Office of Innovation and Commercialization
9500 Gilman Drive, Mail Code 0910
University of California
La Jolla, CA 92093-0910
[email protected]
This software program and documentation are copyrighted by The Regents of the University of California. The software program and documentation are supplied “as is”, without any accompanying services from The Regents. The Regents does not warrant that the operation of the program will be uninterrupted or error-free. The end-user understands that the program was developed for research purposes and is advised not to rely exclusively on the program for any reason.
IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. THE UNIVERSITY OF CALIFORNIA SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE PROVIDED HEREUNDER IS ON AN “AS IS” BASIS, AND THE UNIVERSITY OF CALIFORNIA HAS NO OBLIGATIONS TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
Content type
Image
Digest
sha256:ef28997db…
Size
850.2 MB
Last updated
about 2 years ago
docker pull kgaultonlab/t1grs