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bcbio / bcbio-nextgen-vm

Run bcbio-nextgen genomic sequencing analyses using isolated containers and virtual machines
MIT License
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docker image ModuleNotFoundError #192

Open ltnetcase opened 3 years ago

ltnetcase commented 3 years ago

When I try to install bcbio-nextgen-vm with fresh install, I got the following error (run again the same command):

$ bcbio_vm.py --datadir=/GeneCloud001/sysadmin/bcbio-data install --data --tools --genomes GRCh37 --aligners bwa --core 10 Retrieving bcbio-nextgen docker image with code and tools Using default tag: latest Trying to pull repository quay.io/bcbio/bcbio-vc ... latest: Pulling from quay.io/bcbio/bcbio-vc Digest: sha256:cc44e242be9875bea6542b706033897279aa4301cf4800d25de8bb2e51e57bdc Status: Image is up to date for quay.io/bcbio/bcbio-vc:latest [2020-10-28T02:58Z] DEBUG: Running in docker container: d4d571b2164bb9342782397f2bce4116f49aadfa29ec8a07d9bc4136d6340029 [2020-10-28T02:58Z] DEBUG: docker attach --no-stdin d4d571b2164bb9342782397f2bce4116f49aadfa29ec8a07d9bc4136d6340029 [2020-10-28T02:58Z] DEBUG: Traceback (most recent call last): [2020-10-28T02:58Z] DEBUG: File "/usr/local/bin/bcbio_nextgen.py", line 34, in [2020-10-28T02:58Z] DEBUG: from bcbio.setpath import prepend_bcbiopath [2020-10-28T02:58Z] DEBUG: ModuleNotFoundError: No module named 'bcbio' [2020-10-28T02:58Z] ERROR: Uncaught exception occurred Traceback (most recent call last): File "/usr/local/opt/anaconda/envs/bcbio/lib/python3.7/site-packages/bcbio/provenance/do.py", line 26, in run _do_run(cmd, checks, log_stdout, env=env) File "/usr/local/opt/anaconda/envs/bcbio/lib/python3.7/site-packages/bcbio/provenance/do.py", line 106, in _do_run raise subprocess.CalledProcessError(exitcode, error_msg) subprocess.CalledProcessError: Command 'docker attach --no-stdin d4d571b2164bb9342782397f2bce4116f49aadfa29ec8a07d9bc4136d6340029 Traceback (most recent call last): File "/usr/local/bin/bcbio_nextgen.py", line 34, in from bcbio.setpath import prepend_bcbiopath ModuleNotFoundError: No module named 'bcbio' ' returned non-zero exit status 1. Stopping docker container Traceback (most recent call last): File "/usr/local/opt/anaconda/envs/bcbio/bin/bcbio_vm.py", line 354, in args.func(args) File "/usr/local/opt/anaconda/envs/bcbio/bin/bcbio_vm.py", line 40, in cmd_install install.full(args, devel.DOCKER) File "/usr/local/opt/anaconda/envs/bcbio/lib/python3.7/site-packages/bcbiovm/docker/install.py", line 29, in full manage.run_bcbio_cmd(args.image, dmounts, ["upgrade"]) File "/usr/local/opt/anaconda/envs/bcbio/lib/python3.7/site-packages/bcbiovm/docker/manage.py", line 48, in run_bcbio_cmd raise e File "/usr/local/opt/anaconda/envs/bcbio/lib/python3.7/site-packages/bcbiovm/docker/manage.py", line 44, in run_bcbio_cmd log_stdout=True) File "/usr/local/opt/anaconda/envs/bcbio/lib/python3.7/site-packages/bcbio/provenance/do.py", line 26, in run _do_run(cmd, checks, log_stdout, env=env) File "/usr/local/opt/anaconda/envs/bcbio/lib/python3.7/site-packages/bcbio/provenance/do.py", line 106, in _do_run raise subprocess.CalledProcessError(exitcode, error_msg) subprocess.CalledProcessError: Command 'docker attach --no-stdin d4d571b2164bb9342782397f2bce4116f49aadfa29ec8a07d9bc4136d6340029 Traceback (most recent call last): File "/usr/local/bin/bcbio_nextgen.py", line 34, in from bcbio.setpath import prepend_bcbiopath ModuleNotFoundError: No module named 'bcbio'

Can anyone help to fix this issue? It seems like an old issue here

hackdna commented 3 years ago

More information here: https://github.com/bcbio/bcbio_docker/issues/4