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Update README.md
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@xiaoliz0
xiaoliz0 authored Nov 28, 2023
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Expand Up @@ -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.
Expand Down Expand Up @@ -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

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