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Last pushed: 2 months ago
Short Description
Docker Image For microRNA Gene Expression Prediction Model Pipeline
Full Description

Docker Image That Contains microRNA Gene Expression Prediction pipeline

Docker image

The Docker image can be downloaded by running the following command

docker pull jiamaozheng/microrna_prediction_models_docker

Docker File

Is available at here

Pipeline

Is available at here

Prerequisites

Create an input directory by running a script

Prepare the input files with the following formats and place them in appropriate input directory

Running Docker Image

# Run a Docker image as a Container and mounts the input directory in the Container 
docker run -v /Volumes/im-lab/nas40t2/jiamao/Projects/microRNA/model_pipeline/model_pipeline/microRNA_gene_expression_prediction_model_pipeline:/microRNA_gene_expression_prediction_model_pipeline -it jiamaozheng/microrna_prediction_models_docker

Running Pipeline Inside the Docker Container

./run.py \
--project_name gEUVADIS_LCL_miRNA \
--molecular_type miRNA \
--alpha 0.5 \
--snpset 1KG_snps \

--expression_path ../input_mirna/expression_phenotypes/miRNA_CTR_Exp.RDS \
--genotype_path ../input_mirna/genotype/ \
--gene_annot_path ../input_mirna/gene_annotation/miRBase_miRNA_gene_annotation.RDS \
--snp_annot_path ../input_mirna/snp_annotation/gEUVADIS.SNP.annotation.RDS \
--intermediate_path ../input_mirna/intermediate/ \ 

--results_output_path ../output_mirna/

More command line examples

Docker Pull Command
Owner
jiamaozheng

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