bcbio_vm.py aws cluster start give 'ansible_utils' is not defined

[apastore]

Hi Brad, I was just trying the aws implemetation of bcbio and got this error. Thanks!

Traceback (most recent call last):
File "/cbio/ski/abdelwao/home/pastore/bin/bcbio_vm.py", line 4, in
import('pkg_resources').run_script('bcbio-nextgen-vm==0.1.0a0', 'bcbio_vm.py')
File "/cbio/ski/abdelwao/home/pastore/nobackup/bcbio/anaconda/envs/bcbio-vm/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/init.py", line 744, in run_script
File "/cbio/ski/abdelwao/home/pastore/nobackup/bcbio/anaconda/envs/bcbio-vm/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/init.py", line 1506, in run_script
File "/cbio/ski/abdelwao/home/pastore/nobackup/bcbio/anaconda/envs/bcbio-vm/lib/python2.7/site-packages/bcbio_nextgen_vm-0.1.0a0-py2.7.egg/EGG-INFO/scripts/bcbio_vm.py", line 322, in

File "/cbio/ski/abdelwao/home/pastore/nobackup/bcbio/anaconda/envs/bcbio-vm/lib/python2.7/site-packages/bcbio_nextgen_vm-0.1.0a0-py2.7.egg/bcbiovm/aws/icel.py", line 184, in create
File "/cbio/ski/abdelwao/home/pastore/nobackup/bcbio/anaconda/envs/bcbio-vm/lib/python2.7/site-packages/bcbio_nextgen_vm-0.1.0a0-py2.7.egg/bcbiovm/aws/common.py", line 122, in run_ansible_pb
NameError: global name 'ansible_utils' is not defined
[1]+ Exit 1 bcbio_vm.py aws cluster start

[apastore]

this what generate the error
bcbio_vm.py aws icel create

[apastore]

also this generate the same error
bcbio_vm.py aws cluster start

[apastore]

also when I ssh in the cluster with bcbio_vm.py aws cluster ssh
I do not see the /encrypted folder even if I star the cluster without lustre

NFS file system (no Lustre):

mkdir /encrypted/pastorea
mkdir: cannot create directory `/encrypted/pastorea': No such file or directory

Thanks!

[chapmanb]

Thanks for testing this out and sorry about the issues. Practically, it looks like you have an older version of bcbio-vm as this ansible_utils typo was fixed a few months ago (48899e7#diff-858d17d4d306ec011658b187fe3f9020).

More generally, though, we're currently phasing out the custom AWS support in bcbio in favor of using AWS support from projects supporting the common workflow language. We haven't worked a lot on our AWS code in a while and there are better general implementations available we'd like to use like Toil's AWS support.

We're working on building out and testing this and should have more documentation and details soon. If you're AWS needs aren't immediate, waiting for better general support is probably a better plan at this point than trying to use the custom architecture. Would this work for your needs?

[apastore]

Definitely! Thanks a lot for your clarification!

…

Sent from my iPhone

On Oct 21, 2017, at 8:11 PM, Brad Chapman ***@***.***> wrote: Thanks for testing this out and sorry about the issues. Practically, it looks like you have an older version of bcbio-vm as this ansible_utils typo was fixed a few months ago (48899e7#diff-858d17d4d306ec011658b187fe3f9020). More generally, though, we're currently phasing out the custom AWS support in bcbio in favor of using AWS support from projects supporting the common workflow language. We haven't worked a lot on our AWS code in a while and there are better general implementations available we'd like to use like Toil's AWS support. We're working on building out and testing this and should have more documentation and details soon. If you're AWS needs aren't immediate, waiting for better general support is probably a better plan at this point than trying to use the custom architecture. Would this work for your needs? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.