These are scripts to help run tests
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
bin/get_dkfz_resources.sh
Dowload the test sample HCC1143 and place it in the data directory
bin/get_test_resources.sh
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
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
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.