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AmpliconSuite / AmpliconSuite-pipeline

A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
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run_paa_script.sh in Docker has permission problem to write #13

Closed Si-Nan closed 3 years ago

Si-Nan commented 3 years ago

Hi Jens,

I installed PrepareAA and AmpliconArchictect accroding to Readme by docker. But when I run PAA through run_paa_docker.py with CNV bed and bam(coordination sorted), it occurs something wrong about Permission.

$PAA -o ~/r2/paa-output -s test -t 5 --cnv_bed ~/r2/data/filter1.SCNA --sorted_bam ~/r2/data/R19059763LD01-18s18941-eHCC1.mkdup.realn.recal.bam  --no_AA
Creating a docker script with the following argstring:
--ref hg19 -t 5 --cngain 4.999999 --cnsize_min 50000 --downsample 10 -s test -o /home/output --sorted_bam /home/bam_dir/R19059763LD01-18s18941-eHCC1.mkdup.realn.recal.bam --cnv_bed /home/bed_dir/filter1.SCNA

docker run  --rm -e AA_DATA_REPO=/home/data_repo -e argstring="$argstring" -v $AA_DATA_REPO:/home/data_repo -v /home/zhaisinan/r2/data:/home/bam_dir -v /home/zhaisinan/r2/data:/home/bed_dir -v /home/zhaisinan/r2/paa-output:/home/output -v /home/zhaisinan/r2/:/home/programs/mosek/8/licenses jluebeck/prepareaa  bash /home/run_paa_script.sh

/home/run_paa_script.sh: line 9: /home/output/docker_home_manifest.log: Permission denied
/home/run_paa_script.sh: line 10: /home/output/PAA_stdout.log: Permission denied

the two lines for this error are:

ls /home > /home/output/docker_home_manifest.log
python programs/PrepareAA-master/PrepareAA.py $argstring &> /home/output/PAA_stdout.log

When I run PAA interactively, the user is root in the docker, and I succeed to implement the first line code: ls /home > /home/output/docker_home_manifest.log I don't konw why it fell with script.

Firstly, I tried to change permission of this output directory and made a new image. but it did't work. Then, I changed add --privileged=true option in run_paa_docker.py to gave it a high permission, but it did't work, too...

I am very new to docker and I have google and read a book for docker for the error. Maybe I did some stupid things, but I don't realize...

Could you please give me a hand?

Best, Sinan

Si-Nan commented 3 years ago

Sorry, I realized the reason of error. It's because of the permission of the directories which mounted to the docker are low. I went in the wrong direction before.