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FRED-2 / OptiType

Precision HLA typing from next-generation sequencing data
BSD 3-Clause "New" or "Revised" License
180 stars 74 forks source link

Commands for Singularity Bootstrap of Docker Image #114

Open ilovesquishy opened 4 years ago

ilovesquishy commented 4 years ago

Hello! I'm trying to run the docker image via singularity bootstrap, since the HPC does not provide root access for docker. What would the command equivalent for -v, -t, and -i, -o in the Docker commands be, for Singularity?

singularity build optitype.simg docker://fred2/optitype

Trying singularity exec -B path1:/data -B path2:/output optitype_fred2.simg -i /data:/bam.name -d -o /output/ Gives the error that -i is not a command for exec.

jayon-lihm commented 3 years ago

Hi I had the same problem, and I recently figured it is needed to type the python script name to invoke Optitype as below:

singularity exec --bind $final_output_path:/data $opti_image OptiTypePipeline.py -i /data/sample_1_fished.fastq /data/sample_2_fished.fastq -d -v -o /data