search

KolmogorovLab / hapdup

Pipeline to convert a haploid assembly into diploid
Other
85 stars 8 forks source link

Singularity #1

Closed GuillaumeHolley closed 2 years ago

GuillaumeHolley commented 2 years ago

Hi,

Thank you for this tool, I am really excited to try it! Would it be possible to have hapdup available as a Singularity image or to have the Docker image available online in a container repo (such that it can be converted to a Singularity image with a singularity pull)?

Thanks, Guillaume

kishwarshafin commented 2 years ago

@GuillaumeHolley ,

The docker is available on docker hub:

cd directory_with_assembly_and_alignment
HD_DIR=`pwd`
docker run -v $HD_DIR:$HD_DIR --ipc=host -u `id -u`:`id -g` mkolmogo/hapdup:0.2 hapdup --assembly $HD_DIR/assembly.fasta --bam $HD_DIR/lr_mapping.bam --out-dir $HD_DIR/hapdup -t 64

You can use singularity similarly as you use for PEPPER-Margin-DeepVariant

mikolmogorov commented 2 years ago

Thanks @kishwarshafin !

@GuillaumeHolley let us know if you have any issues - I will update the manual soon to reflect this.

GuillaumeHolley commented 2 years ago

Thanks @kishwarshafin @fenderglass,

I just did a singularity pull docker://mkolmogo/hapdup:0.2 to pull the Singularity image out of Docker Hub.

Guillaume