From 53e96d9d1dd49967576657b974ceb067dffdd2bf Mon Sep 17 00:00:00 2001 From: Xiaoli Zhang <81294502+xiaoliz0@users.noreply.github.com> Date: Tue, 28 Nov 2023 11:44:07 +0100 Subject: [PATCH] Update README.md --- README.md | 39 ++++++++++++++++++++------------------- 1 file changed, 20 insertions(+), 19 deletions(-) diff --git a/README.md b/README.md index 5dd71f4..e74cb13 100644 --- a/README.md +++ b/README.md @@ -18,23 +18,15 @@ Script/PRONTO.py --- The python script. Config/configure_PRONTO.ini --- The configure file. Local changes is needed to set up. In/Templates/MTB_template.pptx --- The template file used for generating PP report. In/InPreD_PRONTO_metadata.txt --- The clinical data file. Reports will be generated for the Sample_id with "Create_report==Y" in this file. -In/MTF/IPD-XXXX_Material Transit Form InPreD NGS.xlsx --- The material file contains all patient personal information. (only OUS) - +In/MTF/IPD-XXXX_Material Transit Form InPreD NGS.xlsx --- The material file contains all patient personal information. (Used by OUS) + OUTPUT: Out/$runID/IPDXXX --- The folder contains all results for this sample. Out/$runID/IPDXXX/extra_files --- The folder contains filter tables during the canculation process, and the patient material file from lab. Out/$runID/IPDXXX/IPDXXX_MTB_report.pptx --- The PP report file. -Out/$runID/IPDXXX/IPDXXX_Remisse_draft.docx --- The remisse draft file for email. (only OUS) +Out/$runID/IPDXXX/IPDXXX_Remisse_draft.docx --- The remisse draft file for email. (Used by OUS) Out/InPreD_PRONTO_metadata_tsoppi.txt --- The file contains clinical data and the SOPPI results for all sample reports. - -IMAGES: -PRONTO_image/PRONTO_docker/Dockerfile --- The file used to build up the docker image. -PRONTO_image/PRONTO_docker/PRONTO_v1_docker_image.tar --- The Docker image file of PRONTO. -PRONTO_image/PRONTO_docker_build.sh --- The script can build a PRONTO docker image "docker_pronto:v1". -PRONTO_image/PRONTO_docker_run.sh --- The script runs a container based on the docker image "docker_pronto:v1". -PRONTO_image/PRONTO_singularity/PRONTO_v1_singularity_image.sif --- The Singularity image file of PRONTO. -PRONTO_image/PRONTO_singularity_run.sh --- The script executes PRONTO command based on the PRONTO Singularity image. - + TESTING: Testing_data/191206_NB501498_0174_AHWCNMBGXC_TSO_500_LocalApp_postprocessing_results.zip --- The testing data from AcroMetrix sample TSOPPI results which only contains the files PRONTO needs. Move this filder into your local TSOPPI result path for testing. Testing_data/InPreD_PRONTO_metadata.txt --- The file contains clinical data of AcroMetrix samples for testing. Move this file into In/ for testing. @@ -64,14 +56,23 @@ Special commands used by OUS: [python3 Script/InPreD_PRONTO.py -m] # PRONTO Docker -PRONTO_image/PRONTO_docker_build.sh -This script is used to build a PRONTO docker image "pronto:v1". +PRONTO docker image is automatically pushed to dockerhub: https://hub.docker.com/r/inpred/pronto +Please download the image with the "latest" tag: [docker pull inpred/pronto:latest] -[PRONTO_image/PRONTO_docker_run.sh] -This script is used to run a container once with command "python Script/InPreD_PRONTO.py" based on the docker image "pronto:v1". This script will ask you to put into your local "TSOPPI results" path, and the reports will be exported to "Out/$runID/IPDXXX" under your "PRONTO_report" folder. +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 $pronto_output_dir:/pronto/Out inpred/pronto:latest python /pronto/Script/PRONTO.py] + +"$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. # PRONTO Singularity -Download PRONTO singularity image or build it based on the PRONTO docker image in your local system. Store the image file under PRONTO_image/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. + +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 $PRONTO_singularity_image_file python /pronto/Script/PRONTO.py] -PRONTO_image/PRONTO_singularity_run.sh -This script is used to execute with command "python Script/InPreD_PRONTO.py" based on the PRONTO Singularity image. This script will ask you to put into your local "TSOPPI results" path, and the reports will be exported to "Out/$runID/IPDXXX" under your "PRONTO_report" folder. +"$tsoppi_data" is the path of your local TSOPPI results, where contains all runs of TSOPPI data not the folder for individual runs. +"$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