Question: Bioblend launches Cloudman but not Galaxy - app status 'yellow'
gravatar for bobbledavidson
3.2 years ago by
Hong Kong
bobbledavidson0 wrote:

Hi all,

I can launch an AWS instance using BioBlend's CloudManInstance.launch_instance() but I can't seem to get Galaxy to launch. 

Code for launching Cloudman (in N.Virginia):

from bioblend.cloudman import CloudManConfig
from bioblend.cloudman import CloudManInstance

cfg=CloudManConfig(access_key='THATSMYACCESSKEY',kwargs={},ramdisk_id=None,placement='',initial_storage_size=20,image_id='ami-a7dbf6ce', kernel_id=None,galaxy_data_option='',cluster_name='bb_test_cluster',instance_type='m1.medium',block_until_ready=True,cluster_type='Galaxy',secret_key='ITSMYSECRETTOO',password='CHANGEPASS',security_groups=['cloudman-sg'],keyname='cloudman_key_pair')

cmi = CloudManInstance.launch_instance(cfg)

Response from cmi.get_status()

{u'disk_usage': {u'total': u'0', u'pct': u'0%', u'used': u'0'}, u'all_fs': [], u'app_status': u'yellow', u'autoscaling': {u'use_autoscaling': False, u'as_max': u'N/A', u'as_min': u'N/A'}, u'snapshot': {u'status': u'None', u'progress': u'None'}, u'cluster_status': u'STARTING', u'dns': u'#', u'instance_status': {u'available': u'0', u'requested': u'0', u'idle': u'0'}, u'data_status': u'yellow'}

I can access the CloudMan page at the instance URL and it tells me that there is no application running. If I try 'cmi.get_galaxy_state()', I get the following error:

Traceback (most recent call last):

  File "<stdin>", line 1, in <module>

  File "/home/gigafig/gigafigcntrl/gfigEnv/lib/python2.7/site-packages/bioblend/cloudman/", line 48, in wrapper

    return func(*args, **kwargs)

  File "/home/gigafig/gigafigcntrl/gfigEnv/lib/python2.7/site-packages/bioblend/cloudman/", line 680, in get_galaxy_state

    return {'status': status['status']}

TypeError: string indices must be integers

I have tried cmi.update() to ensure I'm looking at the latest info,  also cmi.add_nodes(1) which adds nodes but still returns 'yellow' status for data and apps. cmi.initialized() returns 'True' and cmi.get_machine_status() reports everything running without error. 

Any pointers on what I do to actually kick start Galaxy? 





software error galaxy • 789 views
ADD COMMENTlink written 3.2 years ago by bobbledavidson0
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