Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
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4 weeks ago

enter image description hereHaving an issue trying to use the samtools view gs://mybucket/myfile.bam > myfile.bam when using this command with docker.

Always get the error "samtools view: failed to open "gs://mybucket/myfile.bam" for reading: Protocol not supported"

Although the command works just fine GCP VMs, Im unable to recreate this in a docker container.

samtools gcs • 550 views
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7 days ago
aw7 ▴ 300

This is a bit late, but the first thing to go is to run samtools --version and make sure the docker samtools is configured with the the GCS protocols.

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