gmihaiescu / pcawg-docker-test

Scripts to help test Dockstore tools for PCAWG

Testing environment

Introduction

These are scripts to help run tests

Preparation

To use GNOS put your token key in etc/keyfile.txt since that is where my scripts will try to find it. For the ICGC download client put your token into the icgc-storage-client-1.0.19/conf/application.properties file

Download the DKFZ resources

bin/get_dkfz_resources.sh

Download the Test data

Dowload the test sample HCC1143 and place it in the data directory

bin/get_test_resources.sh

Get Donor using ICGC

Go to https://dcc.icgc.org query for a donor e.g. DO50398. Find the files from the table of files with Data Type Aligned Reads and Strategy WGS e.g. FI31031 and follow the link. Get the Object ID e.g. e09a49a8-6381-55ca-ad62-46290e5b7590. Then type the following command

bin/get_icgc_donor.sh DO50398 e09a49a8-6381-55ca-ad62-46290e5b7590 78d071c5-a0f5-5bd1-8e05-9850bf326e93

IMPORTANT: Make sure you put the Tumor Object ID first and the Normal Object ID second

Get Donor using GNOS

Go to https://dcc.icgc.org query for a donor e.g. DO50398. Find the files from the table of files with Data Type Aligned Reads and Strategy WGS e.g. FI31031 and follow the link. Get the Submitter Bundle ID e.g. 136d60db-bd21-4fbc-9a28-59ea70c06f27. Then type the following command

bin/get_gnos_donor.sh DO50398 136d60db-bd21-4fbc-9a28-59ea70c06f27 0bef43a2-352a-42c6-99ff-d97e2675a527

IMPORTANT: Make sure you put the Tumor Submitter Bundle ID first and the Normal Submitter Bundle ID second

Run the test

Decide on the workflow and sample. Workflows are Sanger, DKFZ, and Delly, and samples can be the test sample HCC1143 or any of the donors you prepared

bin/run_test.sh DKFZ HCC1143

or

bin/run_test.sh Delly DO50398

Note that to run DKFZ you need to have ran Delly before so the bedpe file is produced

bin/run_test.sh DKFZ DO50398

The results will be under tests/<workflow>/<sample>/output/<sample>.* for example tests/Sanger/HCC1143/output/HCC1143.somatic.snv.mnv.tar.gz After the process is finished you may want to remove the directory tests/<workflow>/<sample>/datadir/ since it holds a copy of the input files.