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bcbio / bcbio-nextgen-vm

Run bcbio-nextgen genomic sequencing analyses using isolated containers and virtual machines
MIT License
65 stars 17 forks source link

ImportError: No module named callbacks #168

Closed PatrickJReed closed 6 years ago

PatrickJReed commented 6 years ago

Hi All, Im installing bcbio_vm on a google instance. Everthing installed cleanly. Then I ran bcbio_vm.py install --wrapper and that finished cleanly.

but now im getting the following error:

patrickjenningsreed@bcbio-1:~$ bcbio_vm.py Traceback (most recent call last): File "/usr/local/bin/bcbio_vm.py", line 4, in import('pkg_resources').run_script('bcbio-nextgen-vm==0.1.0a0', 'bcbio_vm.py') File "/home/patrickjenningsreed/install/bcbio-vm/anaconda/lib/python2.7/site-packages/pkg_resources/init.py", line 658, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/patrickjenningsreed/install/bcbio-vm/anaconda/lib/python2.7/site-packages/pkg_resources/init.py", line 1445, in run_script exec(script_code, namespace, namespace) File "/home/patrickjenningsreed/install/bcbio-vm/anaconda/lib/python2.7/site-packages/bcbio_nextgen_vm-0.1.0a0-py 2.7.egg/EGG-INFO/scripts/bcbio_vm.py", line 27, in

File "build/bdist.linux-x86_64/egg/bcbiovm/aws/cluster.py", line 8, in File "build/bdist.linux-x86_64/egg/bcbiovm/aws/bootstrap.py", line 7, in File "build/bdist.linux-x86_64/egg/bcbiovm/aws/common.py", line 9, in ImportError: No module named callbacks

chapmanb commented 6 years ago

Patrick; Apologies about the issue with this. I dug into the problem and it looks like the latest version of conda is extra aggressive with dependency upgrades and results in downgrading the bcbio-nextgen-vm package due to a pin, causing the error from the old version. I pushed a fix and will update the bioconda package with this to avoid it in the future, but you can fix your version now with:

bcbiovm_conda install -c conda-forge -c bioconda bcbio-nextgen-vm bcbio-nextgen cwltool arvados-cwl-runner toil  rabix-bunny

and then a second time after the new bioconda package gets built tomorrow to be future proof for new --wrapper updates. Sorry again about the issue and thanks for the detailed report to track it down.

PatrickJReed commented 6 years ago

Thanks for the quick response Brad. Im going to close https://github.com/bcbio/bcbio-nextgen/issues/2353 under the assumption that bcbio_vm is the best way to go on google cloud. Cheers.