def setup(params, *args, **kw):
docker_params = read_config('runtime-bisque.cfg', "docker")
if not asbool(docker_params.get('docker.enabled', False)):
print "No Docker available... cannot set up module."
return 1
try:
# clone Dream.3D UCSB repo and build Docker image
tmp_dir = tempfile.mkdtemp()
print "Cloning code into %s..." % tmp_dir
p = Popen([
'git', 'clone', '[email protected]:wlenthe/UCSB_DREAM3D',
'%s/source' % tmp_dir
],
stdout=PIPE)
if p.wait() != 0:
print "Dream.3D repo could not be cloned... cannot set up module."
return 1
# build Docker image
print "Building Dream.3D docker image..."
p = Popen([
'timeout', '-s', 'SIGKILL', '120m', 'docker', 'build', '--tag',
'dream3d_ucsb',
'%s/source' % tmp_dir
],
stdout=PIPE)
while True:
line = p.stdout.readline()
if line == '':
break
m = re.search('\[[ ]*[0-9]+%\]', line)
if m:
print '\r\r\r\r\r\r',
print m.group(0),
sys.stdout.flush()
print
if p.wait() != 0:
print "Dream.3D image could not be built... cannot set up module."
return 1
python_setup('Dream3D.py', params=params)
docker_setup('bisque_dream3d_ucsb',
'Dream3D',
'dream3d_ucsb',
params=params)
finally:
# delete tmp_dir
shutil.rmtree(tmp_dir)
import sys
from bq.setup.module_setup import python_setup, read_config
def setup(params, *args, **kw):
python_setup('PythonScriptWrapper.py', params=params)
if __name__ == "__main__":
params = read_config('runtime-bisque.cfg')
if len(sys.argv) > 1:
params = eval(sys.argv[1])
sys.exit(setup(params))
# Install script for PlanteomeSegmenter
import sys
from bq.setup.module_setup import matlab_setup, read_config, ensure_matlab, mex_compile, docker_setup
def setup(params, *args, **kw):
ensure_matlab(params)
mex_compile(['vrl_gc.cpp'], where='vrl_tools/maxflow_kolmogorov')
matlab_setup(['PlanteomeSegmenter', '-a', 'vrl_tools'], params=params)
docker_setup('imagematting', 'PlanteomeSegmenter', 'matlab_runtime', params=params)
if __name__ =="__main__":
params = read_config('runtime-bisque.cfg')
if len(sys.argv)>1:
params = eval (sys.argv[1])
sys.exit(setup(params))
