def getVmdEnviron():
""" Return the proper environ to launch VMD.
VMD_HOME variable is read from the ~/.config/scipion.conf file.
"""
environ = Environ(os.environ)
environ.set("PATH", os.path.join(os.environ["VMD_HOME"], "bin"), position=Environ.BEGIN)
return environ
def testInitialVolumeSelector(self):
def _runVolumeSelector(doGpu=False, label=''):
print label
volSelectorProt = self.newProtocol(ProtInitialVolumeSelector,
targetResol=28.32,
numberOfIterations=15,
numberOfMpi=3, numberOfThreads=1)
volSelectorProt.setObjLabel(label)
volSelectorProt.inputParticles.set(self.protImport.outputParticles)
volSelectorProt.inputVolumes.set(self.protImportVol.outputVolumes)
volSelectorProt.doGpu.set(doGpu)
self.launchProtocol(volSelectorProt)
return volSelectorProt
def _checkAsserts(relionProt):
self.assertIsNotNone(relionProt.outputVolumes, "There was a "
"problem with "
"Initial Volume "
"Selector")
environ = Environ(os.environ)
cudaPath = environ.getFirst(('RELION_CUDA_LIB', 'CUDA_LIB'))
if cudaPath is not None and os.path.exists(cudaPath):
volSelGpu = _runVolumeSelector(True, "Run Volume Selector GPU")
_checkAsserts(volSelGpu)
else:
volSelNoGPU = _runVolumeSelector(False, "Volume Selector No GPU")
_checkAsserts(volSelNoGPU)
def getEnviron(cls):
""" Load the environment variables needed for Imagic.
IMAGIC_ROOT is set to IMAGIC_HOME MPI-related vars
are set if IMAGIC_HOME/openmpi path exists
IMAGIC_BATCH is needed for batch files to work.
"""
env = Environ(os.environ)
env.update({
'IMAGIC_ROOT': cls.getHome(),
'IMAGIC_BATCH': "1",
})
env.set('LD_LIBRARY_PATH', cls.getHome('lib'), env.BEGIN)
mpidir = cls.getHome('openmpi')
if os.path.exists(mpidir):
env.update({
'MPIHOME': mpidir,
'MPIBIN': mpidir + '/bin',
'OPAL_PREFIX': mpidir
})
env.set('PATH', mpidir + '/bin', env.BEGIN)
else:
print("Warning: IMAGIC_ROOT directory (", cls.getHome(),
") does not contain openmpi folder.\n",
"No MPI support will be enabled.")
return env
def testInitialVolumeSelector(self):
def _runVolumeSelector(doGpu=False, label=''):
print label
volSelectorProt = self.newProtocol(ProtInitialVolumeSelector,
targetResol=28.32,
numberOfIterations=15,
numberOfMpi=3,
numberOfThreads=1)
volSelectorProt.setObjLabel(label)
volSelectorProt.inputParticles.set(self.protImport.outputParticles)
volSelectorProt.inputVolumes.set(self.protImportVol.outputVolumes)
volSelectorProt.doGpu.set(doGpu)
self.launchProtocol(volSelectorProt)
return volSelectorProt
def _checkAsserts(relionProt):
self.assertIsNotNone(
relionProt.outputVolumes, "There was a "
"problem with "
"Initial Volume "
"Selector")
volSelNoGPU = _runVolumeSelector(False, "Volume Selector No GPU")
_checkAsserts(volSelNoGPU)
environ = Environ(os.environ)
cudaPath = environ.getFirst(('RELION_CUDA_LIB', 'CUDA_LIB'))
if cudaPath is not None and os.path.exists(cudaPath):
volSelGpu = _runVolumeSelector(True, "Run Volume Selector GPU")
_checkAsserts(volSelGpu)
def getEnviron(cls):
""" Setup the environment variables needed to launch Ethan. """
environ = Environ(os.environ)
environ.update({'PATH': Plugin.getHome()}, position=Environ.BEGIN)
return environ
def getChimeraEnviron():
""" Return the proper environ to launch chimera.
CHIMERA_HOME variable is read from the ~/.config/scipion.conf file.
"""
environ = Environ(os.environ)
environ.set('PATH', os.path.join(os.environ['CHIMERA_HOME'], 'bin'),
position=Environ.BEGIN)
return environ
def getVmdEnviron():
""" Return the proper environ to launch VMD.
VMD_HOME variable is read from the ~/.config/scipion.conf file.
"""
environ = Environ(os.environ)
environ.set('PATH', os.path.join(os.environ['VMD_HOME'], 'bin'),
position=Environ.BEGIN)
return environ
def getCudaLib(environ=None, useMC2=False):
if environ is None:
environ = Environ(os.environ)
if useMC2:
return environ.getFirst((MOTIONCOR2_CUDA_LIB, CUDA_LIB))
else:
return environ.getFirst((MOTIONCORR_CUDA_LIB, CUDA_LIB))
def getCudaLib(environ=None, useMC2=False):
if environ is None:
environ = Environ(os.environ)
if useMC2:
return environ.getFirst((MOTIONCOR2_CUDA_LIB, CUDA_LIB))
else:
return environ.getFirst((MOTIONCORR_CUDA_LIB, CUDA_LIB))
def getEnviron(xmippFirst=True):
""" Create the needed environment for Xmipp programs. """
environ = Environ(os.environ)
pos = Environ.BEGIN if xmippFirst else Environ.END
environ.update(
{"PATH": join(os.environ["XMIPP_HOME"], "bin"), "LD_LIBRARY_PATH": join(os.environ["XMIPP_HOME"], "lib")},
position=pos,
)
return environ
def getEnviron(xmippFirst=True):
""" Create the needed environment for Bsoft programs. """
environ = Environ(os.environ)
pos = Environ.BEGIN if xmippFirst else Environ.END
environ.update({
'PATH': os.path.join(os.environ['BSOFT_HOME'], 'bin'),
#'LD_LIBRARY_PATH': join(os.environ['BSOFT_HOME'], 'lib')
}, position=pos)
return environ
def getEnviron(xmippFirst=True):
""" Create the needed environment for Xmipp programs. """
environ = Environ(os.environ)
pos = Environ.BEGIN if xmippFirst else Environ.END
environ.update({
'PATH': join(os.environ['XMIPP_HOME'], 'bin'),
'LD_LIBRARY_PATH': join(os.environ['XMIPP_HOME'], 'lib')
}, position=pos)
return environ
def getEnviron():
""" Setup the environment variables needed to launch Relion. """
environ = Environ(os.environ)
environ.update({
'PATH': join(os.environ['RELION_HOME'], 'bin'),
'LD_LIBRARY_PATH': join(os.environ['RELION_HOME'], 'lib') + ":" + join(os.environ['RELION_HOME'], 'lib64'),
'SCIPION_MPI_FLAGS': os.environ.get('RELION_MPI_FLAGS', ''),
}, position=Environ.BEGIN)
return environ
def getEnviron(cls):
""" Setup the environment variables needed to launch localrec. """
environ = Environ(os.environ)
environ.update(
{
'PATH': getXmippPath('bin'),
'LD_LIBRARY_PATH': getXmippPath('lib')
},
position=Environ.BEGIN)
return environ
def getEnviron(cls):
environ = Environ(os.environ)
environ.update(
{
'PATH': cls.getHome('bin'),
'LD_LIBRARY_PATH': cls.getHome('lib')
},
position=Environ.BEGIN)
return environ
def getEnviron(cls):
""" Setup the environment variables needed to launch 3DFSC. """
environ = Environ(os.environ)
if 'PYTHONPATH' in environ:
# this is required for python virtual env to work
del environ['PYTHONPATH']
environ.update({'PATH': cls.getHome('ThreeDFSC')},
position=Environ.BEGIN)
return environ
def getEnviron(cls):
""" Setup the environment variables needed to launch Appion. """
environ = Environ(os.environ)
environ.update({
'PATH': Plugin.getHome(),
'LD_LIBRARY_PATH': str.join(cls.getHome(), 'appionlib')
+ ":" + cls.getHome(),
}, position=Environ.BEGIN)
return environ
def getEnviron():
""" Return the envirion settings to run dosefgpu programs. """
""" Setup the environment variables needed to launch Relion. """
MOTIONCORR_HOME = os.environ.get('MOTIONCORR_HOME',
join(os.environ['EM_ROOT'], 'motioncorr'))
environ = Environ(os.environ)
environ.update({
'PATH': join(MOTIONCORR_HOME, 'bin'),
'LD_LIBRARY_PATH': join(os.environ.get('MOTIONCORR_CUDA_LIB', ''))
}, position=Environ.BEGIN)
return environ
def getEnviron():
""" Setup the environment variables needed to launch Appion. """
environ = Environ(os.environ)
if 'DOGPICKER_HOME' in environ:
environ.update({
'PATH': os.environ['DOGPICKER_HOME'],
'LD_LIBRARY_PATH': join(os.environ['DOGPICKER_HOME'], 'appionlib') + ":" + os.environ['DOGPICKER_HOME'],
}, position=Environ.BEGIN)
else:
#TODO: Find a generic way to warn of this situation
print "DOGPICKER_HOME variable not set on environment."
return environ
def getEnviron():
""" Create the needed environment for Xmipp programs. """
environ = Environ(os.environ)
SIMPLEBIN = os.path.join(os.environ['SIMPLE_HOME'], 'bin')
environ.update({
'SIMPLEBIN': SIMPLEBIN,
'SIMPLEPATH': os.environ['SIMPLE_HOME'],
'SIMPLESYS': os.environ['SIMPLE_HOME'],
'PATH': SIMPLEBIN + os.pathsep + os.path.join(os.environ['SIMPLE_HOME'], 'apps')
},
position=Environ.BEGIN)
return environ
def getEnviron():
""" Return the envirion settings to run dosefgpu programs. """
""" Setup the environment variables needed to launch Relion. """
MOTIONCORR_HOME = os.environ.get('MOTIONCORR_HOME',
join(os.environ['EM_ROOT'], 'motioncorr'))
environ = Environ(os.environ)
environ.update(
{
'PATH': join(MOTIONCORR_HOME, 'bin'),
'LD_LIBRARY_PATH': join(os.environ.get('MOTIONCORR_CUDA_LIB', ''))
},
position=Environ.BEGIN)
return environ
def getEnviron():
""" Setup the environment variables needed to launch Eman. """
environ = Environ(os.environ)
EMAN2DIR = os.environ['EMAN2DIR']
pathList = [os.path.join(EMAN2DIR, d) for d in ['lib', 'bin', 'extlib/site-packages']]
environ.update({
'PATH': join(EMAN2DIR, 'bin'),
'LD_LIBRARY_PATH': os.pathsep.join(pathList),
'PYTHONPATH': os.pathsep.join(pathList),
'EMAN_PYTHON': os.path.join(EMAN2DIR, 'Python/bin/python')
}, position=Environ.REPLACE)
return environ
def getEnviron(cls, bsoftVersion=None):
""" Setup the environment variables needed to launch bsoft.
:param bsoftVersion (optional) pass a version to be used,
otherwise will choose default value for BSOFT_HOME"""
environ = Environ(os.environ)
home = cls.getHomeFromVersion(bsoftVersion)
environ.update({
'PATH': os.path.join(home, 'bin'),
'BSOFT': home
}, position=Environ.BEGIN)
return environ
def getEnviron():
""" Load the environment variables needed for Spider.
If SPIDER_DIR is defined, the bin, man and proc folders will be
defined from it. If not, each of them should be defined separately.
"""
global SPIDER
env = Environ(os.environ)
SPIDER_DIR = env.getFirst(('SPIDER_HOME', 'SPIDER_DIR'), mandatory=True) #
# Scipion
# definition
if SPIDER_DIR is None:
errors = ''
for var in ['SPBIN_DIR', 'SPMAN_DIR', 'SPPROC_DIR']:
if not var in env:
errors += "\n Missing SPIDER variable: '%s'" % var
if len(errors):
print "ERRORS: " + errors
else:
env.update({
'SPBIN_DIR': join(SPIDER_DIR, 'bin') +
'/', # Spider needs this extra slash at the end
'SPMAN_DIR': join(SPIDER_DIR, 'man') + '/',
'SPPROC_DIR': join(SPIDER_DIR, 'proc') + '/'
})
# Get the executable or 'spider' by default
SPIDER = join(env['SPBIN_DIR'], env.get('SPIDER',
'spider_linux_mp_intel64'))
# expand ~ and vars
SPIDER = abspath(os.path.expanduser(os.path.expandvars(SPIDER)))
env.set('PATH', env['SPBIN_DIR'], env.END)
return env
def getEnviron():
""" Setup the environment variables needed to launch Relion. """
environ = Environ(os.environ)
environ.update(
{
'PATH':
join(os.environ['RELION_HOME'], 'bin'),
'LD_LIBRARY_PATH':
join(os.environ['RELION_HOME'], 'lib') + ":" +
join(os.environ['RELION_HOME'], 'lib64'),
'SCIPION_MPI_FLAGS':
os.environ.get('RELION_MPI_FLAGS', ''),
},
position=Environ.BEGIN)
return environ
def getRelionEnviron():
""" Setup the environment variables needed to launch Relion. """
environ = Environ(os.environ)
relionHome = os.environ[LOCALREC_RELION_HOME]
binPath = join(relionHome, 'bin')
libPath = join(relionHome, 'lib') + ":" + join(relionHome, 'lib64')
if not binPath in environ['PATH']:
environ.update({'PATH': binPath,
'LD_LIBRARY_PATH': libPath,
'SCIPION_MPI_FLAGS': os.environ.get(
'RELION_MPI_FLAGS', ''),
}, position=Environ.BEGIN)
return environ
def getEnviron(cls):
""" Setup the environment variables needed to launch localrec. """
environ = Environ(os.environ)
print("getEnvirion(): %s" % os.environ.get(cls.getHome()))
if ('%s' % cls.getHome()) in environ:
environ.update(
{
'PATH': cls.getHome(),
'LD_LIBRARY_PATH': os.environ[cls.getHome()],
},
position=Environ.BEGIN)
else:
# TODO: Find a generic way to warn of this situation
print("%s variable not set on environment." % cls.getHome())
return environ
def getEnviron(cls):
""" Setup the environment variables needed to launch pyseg. """
environ = Environ(os.environ)
pySegDir = cls.getHome()
# Add required disperse path to PATH and pyto path to PYTHONPATH
environ.update({
'PATH':
join(pySegDir, '%s_build' % DISPERSE, 'bin'),
'PYTHONPATH':
join(pySegDir,
'pyseg_system-%s' % DEFAULT_VERSION.replace('v', ''), 'code')
})
return environ
def getEnviron(cls):
""" Setup the environment variables needed to launch aitom. """
environ = Environ(os.environ)
if 'PYTHONPATH' in environ:
# this is required for python virtual env to work
del environ['PYTHONPATH']
return environ
def getMembSegEnviron(cls):
""" Setup the environment variables needed to launch pyseg. """
environ = Environ(os.environ)
runtimePath = cls.getMCRPath()
# Add required disperse path to PATH and pyto path to PYTHONPATH
environ.update({
'LD_LIBRARY_PATH':
os.pathsep.join([
join(runtimePath, 'runtime', 'glnxa64'),
join(runtimePath, 'bin', 'glnxa64'),
join(runtimePath, 'sys', 'os', 'glnxa64'),
join(runtimePath, 'sys', 'opengl', 'lib', 'glnxa64')
])
})
return environ
def getRelionEnviron():
""" Setup the environment variables needed to launch Relion. """
environ = Environ(os.environ)
relionHome = os.environ[LOCALREC_RELION_HOME]
binPath = join(relionHome, 'bin')
libPath = join(relionHome, 'lib') + ":" + join(relionHome, 'lib64')
if not binPath in environ['PATH']:
environ.update(
{
'PATH': binPath,
'LD_LIBRARY_PATH': libPath,
'SCIPION_MPI_FLAGS': os.environ.get('RELION_MPI_FLAGS', ''),
},
position=Environ.BEGIN)
return environ
def getEnviron():
""" Setup the environment variables needed to launch Appion. """
environ = Environ(os.environ)
if 'DOGPICKER_HOME' in environ:
environ.update(
{
'PATH':
os.environ['DOGPICKER_HOME'],
'LD_LIBRARY_PATH':
join(os.environ['DOGPICKER_HOME'], 'appionlib') + ":" +
os.environ['DOGPICKER_HOME'],
},
position=Environ.BEGIN)
else:
#TODO: Find a generic way to warn of this situation
print "DOGPICKER_HOME variable not set on environment."
return environ
def getEnviron():
""" Load the environment variables needed for Spider.
If SPIDER_DIR is defined, the bin, man and proc folders will be
defined from it. If not, each of them should be defined separately.
"""
global SPIDER
env = Environ(os.environ)
SPIDER_PATH = env.getFirst((SPIDER_HOME, SPIDER_DIR), mandatory=True) #
# Scipion
# definition
# env.setInstalled(os.path.exists(SPIDER_DIR))
if SPIDER_PATH is None:
errors = ''
for var in [SPBIN_DIR, SPMAN_DIR, SPPROC_DIR]:
if not var in env:
errors += "\n Missing SPIDER variable: '%s'" % var
if len(errors):
print "ERRORS: " + errors
else:
env.update({SPBIN_DIR: join(SPIDER_PATH, 'bin') + '/', # Spider needs this extra slash at the end
SPMAN_DIR: join(SPIDER_PATH, 'man') + '/',
SPPROC_DIR: join(SPIDER_PATH, 'proc') + '/'
})
# Get the executable or 'spider' by default
SPIDER = join(env[SPBIN_DIR], env.get('SPIDER', 'spider_linux_mp_intel64'))
# expand ~ and vars
SPIDER = abspath(os.path.expanduser(os.path.expandvars(SPIDER)))
env.set('PATH', env[SPBIN_DIR], env.END)
return env
def getEnviron():
""" Setup the environment variables needed to launch Eman. """
environ = Environ(os.environ)
EMAN2DIR = os.environ['EMAN2DIR']
pathList = [os.path.join(EMAN2DIR, d)
for d in ['lib', 'bin', 'extlib/site-packages']]
# This environment variable is used to setup OpenGL (Mesa)
# library in remote desktops
if 'REMOTE_MESA_LIB' in os.environ:
pathList.append(os.environ['REMOTE_MESA_LIB'])
environ.update({
'PATH': join(EMAN2DIR, 'bin'),
'PYTHONPATH': os.pathsep.join(pathList),
'EMAN_PYTHON': os.path.join(EMAN2DIR, 'Python/bin/python')
}, position=Environ.REPLACE)
return environ
def getEnviron():
""" Setup the environment variables needed to launch Eman. """
environ = Environ(os.environ)
EMAN2DIR = os.environ['EMAN2DIR']
pathList = [os.path.join(EMAN2DIR, d)
for d in ['lib', 'bin', 'extlib/site-packages']]
# This environment variable is used to setup OpenGL (Mesa)
# library in remote desktops
if 'REMOTE_MESA_LIB' in os.environ:
pathList.append(os.environ['REMOTE_MESA_LIB'])
environ.update({
'PATH': join(EMAN2DIR, 'bin'),
'LD_LIBRARY_PATH': os.pathsep.join(pathList),
'PYTHONPATH': os.pathsep.join(pathList),
'EMAN_PYTHON': os.path.join(EMAN2DIR, 'Python/bin/python')
}, position=Environ.REPLACE)
return environ
def getEnviron(cls):
""" Setup the environment variables needed to launch pkdp """
environ = Environ(os.environ)
# environ.update({
# 'PATH': Plugin.getHome(),
# 'LD_LIBRARY_PATH': str.join(cls.getHome(), 'pkdplib')
# + ":" + cls.getHome(),
# }, position=Environ.BEGIN)
return environ
def setEmanEnviron():
""" Setup the environment variables needed to launch Eman and
use its modules.
"""
env = Environ(os.environ)
pathList = [
os.path.join(EMAN2DIR, d)
for d in ['lib', 'bin', 'extlib/site-packages']
]
env.update(
{
'PATH': os.path.join(EMAN2DIR, 'bin'),
'LD_LIBRARY_PATH': os.pathsep.join(pathList),
'PYTHONPATH': os.pathsep.join(pathList),
'EMAN_PYTHON': os.path.join(EMAN2DIR, 'Python/bin/python')
},
position=Environ.BEGIN)
os.environ.update(env)
def getEnviron(cls):
""" Setup the environment variables needed to launch Relion. """
environ = Environ(os.environ)
binPath = os.pathsep.join([cls.getHome('bin'), Config.MPI_BINDIR])
libPath = os.pathsep.join([cls.getHome('lib'), cls.getHome('lib64'), pwem.Config.MPI_LIBDIR])
if binPath not in environ['PATH']:
environ.update({'PATH': binPath,
'LD_LIBRARY_PATH': libPath
}, position=Environ.BEGIN)
# Get Relion CUDA library path if defined
cudaLib = cls.getVar(RELIONTOMO_CUDA_LIB, pwem.Config.CUDA_LIB)
environ.addLibrary(cudaLib)
if 'RELION_MPI_LIB' in os.environ:
environ.addLibrary(os.environ['RELION_MPI_LIB'])
if 'RELION_MPI_BIN' in os.environ:
environ.set('PATH', os.environ['RELION_MPI_BIN'],
position=Environ.BEGIN)
return environ
def getEnviron(cls, gpuId='0'):
""" Setup the environment variables needed to launch cryocare. """
environ = Environ(os.environ)
if 'PYTHONPATH' in environ:
# this is required for python virtual env to work
del environ['PYTHONPATH']
environ.update({'CUDA_VISIBLE_DEVICES': gpuId})
cudaLib = environ.get(CRYOCARE_CUDA_LIB, pwem.Config.CUDA_LIB)
environ.addLibrary(cudaLib)
return environ
def getEnviron(useMC2=False):
""" Return the environ settings to run motioncorr programs. """
environ = Environ(os.environ)
if exists(MOTIONCORR_PATH) and not useMC2:
environ.update({'PATH': join(os.environ['MOTIONCORR_HOME'], 'bin')},
position=Environ.BEGIN)
if exists(MOTIONCOR2_PATH):
environ.update({'PATH': join(os.environ['MOTIONCOR2_HOME'], 'bin')},
position=Environ.BEGIN)
cudaLib = getCudaLib(environ, useMC2)
environ.addLibrary(cudaLib)
return environ
def test_Environ(self):
""" Test the Environ class with its utilities. """
from pyworkflow.utils import Environ
env = Environ({'PATH': '/usr/bin:/usr/local/bin',
'LD_LIBRARY_PATH': '/usr/lib:/usr/lib64'
})
env1 = Environ(env)
env1.set('PATH', '/usr/local/xmipp')
self.assertEqual(env1['PATH'],'/usr/local/xmipp')
self.assertEqual(env1['LD_LIBRARY_PATH'], env['LD_LIBRARY_PATH'])
env2 = Environ(env)
env2.set('PATH', '/usr/local/xmipp', position=Environ.BEGIN)
self.assertEqual(env2['PATH'],'/usr/local/xmipp' + os.pathsep + env['PATH'])
self.assertEqual(env2['LD_LIBRARY_PATH'], env['LD_LIBRARY_PATH'])
env3 = Environ(env)
env3.update({'PATH': '/usr/local/xmipp',
'LD_LIBRARY_PATH': '/usr/local/xmipp/lib'},
position=Environ.END)
self.assertEqual(env3['PATH'],env['PATH'] + os.pathsep + '/usr/local/xmipp')
self.assertEqual(env3['LD_LIBRARY_PATH'],env['LD_LIBRARY_PATH'] + os.pathsep + '/usr/local/xmipp/lib')
def getChimeraEnviron():
""" Return the proper environ to launch chimera.
CHIMERA_HOME variable is read from the ~/.config/scipion.conf file.
"""
environ = Environ(os.environ)
environ.set('PATH', os.path.join(os.environ['CHIMERA_HOME'], 'bin'),
position=Environ.BEGIN)
if "REMOTE_MESA_LIB" in os.environ:
environ.set('LD_LIBRARY_PATH', os.environ['REMOTE_MESA_LIB'],
position=Environ.BEGIN)
return environ
def getEnviron(useMC2=False):
""" Return the environ settings to run motioncorr programs. """
environ = Environ(os.environ)
if exists(MOTIONCORR_PATH) and not useMC2:
environ.update({'PATH': join(os.environ['MOTIONCORR_HOME'], 'bin')},
position=Environ.BEGIN)
if exists(MOTIONCOR2_PATH):
environ.update({'PATH': join(os.environ['MOTIONCOR2_HOME'], 'bin')},
position=Environ.BEGIN)
cudaLib = getCudaLib(environ, useMC2)
environ.addLibrary(cudaLib)
return environ
def getEnviron():
""" Setup the environment variables needed to launch Relion. """
environ = Environ(os.environ)
relionHome = os.environ[RELION_HOME]
binPath = join(relionHome, 'bin')
libPath = join(relionHome, 'lib') + ":" + join(relionHome, 'lib64')
if not binPath in environ['PATH']:
environ.update({'PATH': binPath,
'LD_LIBRARY_PATH': libPath,
'SCIPION_MPI_FLAGS': os.environ.get('RELION_MPI_FLAGS', ''),
}, position=Environ.BEGIN)
# Take Scipion CUDA library path
cudaLib = environ.getFirst(('RELION_CUDA_LIB', 'CUDA_LIB'))
environ.addLibrary(cudaLib)
return environ
def getImagicHomeDir():
env = Environ(os.environ)
imagicdir = env.getFirst((IMAGIC_HOME, IMAGIC_DIR), mandatory=True) #
# Scipion
# definition
return env, imagicdir
