Update README.md

InPreD · Nov 28, 2023 · 91c0b33 · 91c0b33
1 parent 53e96d9
commit 91c0b33
Showing 1 changed file with 8 additions and 6 deletions.
diff --git a/README.md b/README.md
@@ -57,7 +57,7 @@ Special commands used by OUS:
 
 # PRONTO Docker
 PRONTO docker image is automatically pushed to dockerhub: https://hub.docker.com/r/inpred/pronto        
-Please download the image with the "latest" tag: [docker pull inpred/pronto:latest]                 
+Please download the image with the latest tag: [docker pull inpred/pronto:latest]                 
 
 Run PRONTO with docker image:                                                                        
 [sudo docker run --rm -it -v $tsoppi_data:/pronto/tsoppi_data -v $InPreD_PRONTO_metadata_file:/pronto/In/InPreD_PRONTO_metadata.txt -v $pronto_output_dir:/pronto/Out inpred/pronto:latest python /pronto/Script/PRONTO.py]       
@@ -67,12 +67,14 @@ Run PRONTO with docker image:
 "$pronto_output_dir" is the path in your local environment to store the reports generated by PRONTO.
 
 # PRONTO Singularity
-Download PRONTO docker image in the dockerhub with the "latest" tag: [docker pull inpred/pronto:latest]                   
-Generate PRONTO Singularity image by conversion from the Docker image.          
+Download PRONTO docker image in the dockerhub with the latest tag: [docker pull inpred/pronto:latest]                                                         
+Save the PRONTO docker image to a tar file: [docker save -o PRONTO_docker_image.tar inpred/pronto:latest]                                             
+Generate PRONTO Singularity image by conversion from the docker image file. Example command:                                                   
+[singularity build --disable-cache --tmpdir $SINGULARITY_TMP $dir/PRONTO_singularity_image.sif docker-archive://$dir/PRONTO_docker_image.tar]     
 
-Run PRONTO image with Singularity:                                           
-[singularity exec --no-home -B $tsoppi_data:/pronto/tsoppi_data -B $InPreD_PRONTO_metadata_file:/pronto/In/InPreD_PRONTO_metadata.txt -B $pronto_output_dir:/pronto/Out $PRONTO_singularity_image_file python /pronto/Script/PRONTO.py]                           
+Run PRONTO image with Singularity:                                                                       
+[singularity exec --no-home -B $tsoppi_data:/pronto/tsoppi_data -B $InPreD_PRONTO_metadata_file:/pronto/In/InPreD_PRONTO_metadata.txt -B $pronto_output_dir:/pronto/Out -W $SINGULARITY_TMP $dir/PRONTO_singularity_image.sif python /pronto/Script/PRONTO.py]                           
 
 "$tsoppi_data" is the path of your local TSOPPI results, where contains all runs of TSOPPI data not the folder for individual runs.            
 "$InPreD_PRONTO_metadata_file" is your local InPreD meta data file which contains clinical data for samples.                                      
-"$pronto_output_dir" is the path in your local environment to store the reports generated by PRONTO.p
+"$pronto_output_dir" is the path in your local environment to store the reports generated by PRONTO.py.