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virajbdeshpande / AmpliconArchitect

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.
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Open MrDotOne opened 2 years ago

MrDotOne commented 2 years ago

Finally got AA setup on a pretty beefy server and when i run the docker script i notice that the results are written as root. This may be a silly question but is there a way that the results can be written as the user running the script?

jluebeck commented 2 years ago

Hi,

Yes - we can add an argument to make this choice possible. In the meantime though, one can make a small modification to the docker runscript for AA (or PrepareAA)

In run_aa_docker.sh, modify the last line: docker run --rm -e AA_DATA_REPO=/home/data_repo -e argstring="$argstring" -v $AA_DATA_REPO:/home/data_repo -v $BAM_DIR:/home/bam_dir -v $BED_DIR:/home/bed_dir -v $OUT_DIR:/home/output -v $MOSEKLM_LICENSE_FILE:/home/programs/mosek/8/licenses virajbdeshpande/ampliconarchitect bash /home/run_aa_script.sh

to instead include docker run -u `id -u $USER` --rm -e AA_DATA_REPO= ....

I suppose the alternative is to chown and chgrp all the newly created files at the end of the docker run.

Jens

MrDotOne commented 2 years ago

Thank you for your prompt response. I will check that out immediately, thank you.

MrDotOne commented 2 years ago

I added -uid -u $USER:id -g $USER`` to the run command and it works well.

jluebeck commented 2 years ago

Awesome - good luck with the analyses and let us know if you have any questions. We have wrapped the data pre-processing and post-processing (amplicon classification) steps into a wrapper called PrepareAA which may be of interest.

Jens

MrDotOne commented 2 years ago

I saw that, thank you, and was checking it out. I am actually building this for a researcher who wanted to run this on their Mac laptop.