Hi,
I am not sure how often anyone is monitoring this repo for bug reports, but I wanted to alert you to what is essentially a typo that I discovered. First: I was able to follow your instructions, clone this repo, build the docker container (I used a VM running on Amazon Web Services), and run the PCAWG-QC pipeline on one matched pair of WGS bam files from the ICGC PCAWG project. Thus far (2017-06-13) I have not tried to use the Docker container available in the Dockstore repository (but I have used various other PCAWG Dockers from Dockstore previously). The only real issue I encountered was that in the README.md file the instructions say that the QC_results.tsv file will be written to /home/pcawg/data/results inside the container, and actually, this version of the PCAWG_QC.sh bash script writes the final output to /root/results/ (instead). The relevant lines in the bash script are right near the end. One says 'mkdir -p $HOME/results' and the next line says 'echo "some big long string" > $HOME/results/QC_results.tsv' (I am typing this from memory right now). I confirmed this by (A.) opening an interactive shell on the running container and running the command: 'echo $HOME' (the result was '/root'), and (B.) modifying the docker run command from the README.md file so that the results directory in my host OS was linked to the /root/results directory in the container, and when I made this modification the results file DID appear where I expected it. Oh, I ended up running the docker four separate times on this same dataset, and it did always generate identical results.
Hi,
I am not sure how often anyone is monitoring this repo for bug reports, but I wanted to alert you to what is essentially a typo that I discovered. First: I was able to follow your instructions, clone this repo, build the docker container (I used a VM running on Amazon Web Services), and run the PCAWG-QC pipeline on one matched pair of WGS bam files from the ICGC PCAWG project. Thus far (2017-06-13) I have not tried to use the Docker container available in the Dockstore repository (but I have used various other PCAWG Dockers from Dockstore previously). The only real issue I encountered was that in the README.md file the instructions say that the QC_results.tsv file will be written to /home/pcawg/data/results inside the container, and actually, this version of the PCAWG_QC.sh bash script writes the final output to /root/results/ (instead). The relevant lines in the bash script are right near the end. One says 'mkdir -p $HOME/results' and the next line says 'echo "some big long string" > $HOME/results/QC_results.tsv' (I am typing this from memory right now). I confirmed this by (A.) opening an interactive shell on the running container and running the command: 'echo $HOME' (the result was '/root'), and (B.) modifying the docker run command from the README.md file so that the results directory in my host OS was linked to the /root/results directory in the container, and when I made this modification the results file DID appear where I expected it. Oh, I ended up running the docker four separate times on this same dataset, and it did always generate identical results.