installation error at install_data_s3

[cbergman]

Brad -

Following the recipe here (#5 (comment)) on biolinux7, we encountered the following error with the installation of the test data (install_data_s3):

[SNIP]
INFO: Custom install for 'stampy' end time: 2013-04-04 11:30:05.473528; duration: 0:00:00.295210
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Config end time: 2013-04-04 11:30:05.475118; duration: 0:12:11.246524
INFO: Distribution ubuntu
INFO: Get local environment
INFO: Ubuntu setup
DBG [distribution.py]: Debian-shared setup
DBG [distribution.py]: Source=quantal
DBG [distribution.py]: Checking target distribution ubuntu
[localhost] Login password for 'cbergman':
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/fabric/main.py", line 739, in main
_args, *_kwargs
File "/usr/local/lib/python2.7/dist-packages/fabric/tasks.py", line 316, in execute
multiprocessing
File "/usr/local/lib/python2.7/dist-packages/fabric/tasks.py", line 213, in _execute
return task.run(_args, *_kwargs)
File "/usr/local/lib/python2.7/dist-packages/fabric/tasks.py", line 123, in run
return self.wrapped(_args, *_kwargs)
File "/home/cbergman/tmpbcbio-install/cloudbiolinux/data_fabfile.py", line 66, in install_data_s3
setup_environment()
File "/home/cbergman/tmpbcbio-install/cloudbiolinux/data_fabfile.py", line 41, in setup_environment
_setup_distribution_environment()
File "/home/cbergman/tmpbcbio-install/cloudbiolinux/cloudbio/distribution.py", line 31, in _setup_distribution_environment
_validate_target_distribution(env.distribution, env.get('dist_name', None))
File "/home/cbergman/tmpbcbio-install/cloudbiolinux/cloudbio/distribution.py", line 77, in _validate_target_distribution
if env.edition.short_name in ["minimal"]:
AttributeError: 'str' object has no attribute 'short_name'
Traceback (most recent call last):
File "bcbio_nextgen_install.py", line 188, in
main(parser.parse_args())
File "bcbio_nextgen_install.py", line 43, in main
install_data(cbl["data_fabfile"], fabricrc, biodata)
File "bcbio_nextgen_install.py", line 84, in install_data
"-c", fabricrc, "install_data_s3:%s" % biodata])
File "/usr/lib/python2.7/subprocess.py", line 511, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['fab', '-f', '/home/cbergman/tmpbcbio-install/cloudbiolinux/data_fabfile.py', '-H', 'localhost', '-c', '/home/cbergman/tmpbcbio-install/fabricrc.txt', 'install_data_s3:/home/cbergman/tmpbcbio-install/biodata.yaml']' returned non-zero exit status 1

The tail of our log file reads:

$tail -n 20 bcbio_install_output_log

[localhost] sudo: cp bin/* /home/cbergman/install_directory/bin
[localhost] out: sudo password:
[localhost] out:
[localhost] sudo: cp lib/* /home/cbergman/install_directory/lib
[localhost] out: sudo password:
[localhost] out:
[localhost] run: rm -rf /home/cbergman/tmp/cloudbiolinux

Done.
Disconnecting from localhost... done.
[localhost] Executing task 'install_data_s3'
[localhost] run: cat /proc/version
[localhost] out: Linux version 3.2.0-39-generic (buildd@lamiak) (gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5) ) #62-Ubuntu SMP Thu Feb 28 00:28:53 UTC 2013
[localhost] out:

Disconnecting from localhost... done.
Checking required dependencies
Installing tools...
Installing data...

Thanks again for helping trouble shoot this installation, I think we are getting close to a working solution with your help!

--Casey

[chapmanb]

Casey;
Apologies, this is due to a recent change in CloudBioLinux to help check distributions more carefully and we missed the corresponding fixes in data_fabfile. I pushed the fix to CloudBioLinux, so if you do:

rm -rf tmpbcbio-install/cloudbiolinux

and restart the installer, it will pull in the new CloudBioLinux and keep going happily.

Thank you for all the patience getting this up and running. I appreciate all of the feedback, this is super helpful to make the installer work in as many situations as possible. Please let me know if you run into anything else at all,
Brad

[cbergman]

Hi Brad -

This fix worked, thanks again for the help trouble shooting this step.

-- Casey