def getEnviron(cls):
""" Setup the environment variables needed to launch Eman. """
environ = pwutils.Environ(os.environ)
pathList = [cls.getHome(d) for d in ['lib', 'bin']]
if not cls.isNewVersion():
pathList.append(cls.getHome('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': cls.getHome('bin')},
position=pwutils.Environ.BEGIN)
environ.update(
{
'LD_LIBRARY_PATH': os.pathsep.join(pathList),
'PYTHONPATH': os.pathsep.join(pathList),
'SCIPION_MPI_FLAGS': os.environ.get('EMANMPIOPTS', '')
},
position=pwutils.Environ.REPLACE)
if not cls.isNewVersion():
environ.update({'EMAN_PYTHON': cls.getHome('Python/bin/python')},
position=pwutils.Environ.END)
return environ
def getEnviron(cls):
""" Return the environ settings to run Gctf program. """
environ = pwutils.Environ(os.environ)
# Get Gctf CUDA library path if defined
cudaLib = cls.getVar(GCTF_CUDA_LIB, pwem.Config.CUDA_LIB)
environ.addLibrary(cudaLib)
return environ
def getEnviron(cls, xmippFirst=True):
""" Create the needed environment for Xmipp programs. """
environ = pwutils.Environ(os.environ)
pos = pwutils.Environ.BEGIN if xmippFirst else pwutils.Environ.END
environ.update({
'PATH': pwem.Config.CUDA_BIN,
'LD_LIBRARY_PATH': pwem.Config.CUDA_LIB
}, position=pwutils.Environ.END)
if os.path.isfile(getXmippPath('xmippEnv.json')):
with open(getXmippPath('xmippEnv.json'), 'r') as f:
compilationEnv = json.load(f)
environ.update(compilationEnv, position=pos)
environ.update({
'PATH': getXmippPath('bin'),
'LD_LIBRARY_PATH': getXmippPath('lib'),
'PYTHONPATH': getXmippPath('pylib')
}, position=pos)
environ['XMIPP_HOME'] = getXmippPath()
# Add path to python lib folder
environ.addLibrary(Config.getPythonLibFolder())
return environ
def getEnviron(cls, first=True):
# environ = pwutils.Environ(os.environ)
environ = pwutils.Environ()
pos = pwutils.Environ.BEGIN if first else pwutils.Environ.END
# add to variable
if "DISPLAY" in os.environ:
display = os.environ['DISPLAY']
else:
display = ''
if "HOME" in os.environ:
home = os.environ['HOME']
else:
home = ''
environ.update(
{
'DISPLAY':
display,
'HOME':
home,
'LIBTBX_BUILD':
os.path.join(cls.getHome(), 'build'),
'LIBTBX_OPATH':
os.environ['PATH'],
'PATH':
os.path.join(Plugin.getHome(), 'build', 'bin') + ':/usr/bin:'
'/bin'
},
position=pos)
return environ
def getEnviron(cls):
""" Setup the environment variables needed to launch cryoDRGN. """
environ = pwutils.Environ(os.environ)
if 'PYTHONPATH' in environ:
# this is required for python virtual env to work
del environ['PYTHONPATH']
return environ
def getEnviron():
""" Setup the environment variables needed to launch Relion. """
environ = pwutils.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=pwutils.Environ.BEGIN)
# Take Scipion CUDA library path
cudaLib = environ.getFirst(('RELION_CUDA_LIB', '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=pwutils.Environ.BEGIN)
return environ
def getTensorFlowEnviron(cls):
""" Create the needed environment for XmippTomo programs. """
environ = pwutils.Environ(os.environ)
environ.update({
"TF_FORCE_GPU_ALLOW_GROWTH": "'true'"
}, position=pwutils.Environ.BEGIN)
return environ
def getEnviron(cls):
""" Setup the environment variables needed to launch Eman. """
environ = pwutils.Environ(os.environ)
environ.update({'PATH': cls.getHome('bin')},
position=pwutils.Environ.BEGIN)
return environ
def getEnviron():
environ = pwutils.Environ(os.environ)
environ.update({'RCSBROOT': os.path.join(Plugin.getMaxitHome())},
position=pwutils.Environ.REPLACE)
environ.update({'PATH': os.path.join(Plugin.getMaxitHome(), 'bin')},
position=pwutils.Environ.BEGIN)
return environ
def getEnviron():
""" Return the environ settings to run gautomatch programs. """
environ = pwutils.Environ(os.environ)
# Take Scipion CUDA library path
cudaLib = environ.getFirst(('GAUTOMATCH_CUDA_LIB', 'CUDA_LIB'))
environ.addLibrary(cudaLib)
return environ
def getEnviron(cls):
""" Return the environ settings to run Gautomatch programs. """
environ = pwutils.Environ(os.environ)
# Get Gautomatch CUDA library path if defined
cudaLib = cls.getVar(GAUTOMATCH_CUDA_LIB, pwem.Config.CUDA_LIB)
environ.addLibrary(cudaLib)
return environ
def getEnviron(cls):
""" Return the environment to run motioncor2. """
environ = pwutils.Environ(os.environ)
# Get motioncor2 CUDA library path if defined
cudaLib = cls.getVar(MOTIONCOR2_CUDA_LIB, pwem.Config.CUDA_LIB)
environ.addLibrary(cudaLib)
return environ
def getMGLEnviron(cls):
""" Create the needed environment for MGL Tools programs. """
environ = pwutils.Environ(os.environ)
pos = pwutils.Environ.BEGIN
environ.update({
'PATH': cls.getMGLPath('bin')
}, position=pos)
return environ
def getEnviron():
""" Return the environ settings to run gEMpicker program. """
environ = pwutils.Environ(os.environ)
# Take Scipion CUDA library path
cudaLib = environ.getFirst(('GEMPICKER_CUDA_LIB', 'CUDA_LIB'))
environ.addLibrary(cudaLib)
return environ
def getEnviron(cls):
""" Return the proper environ to launch VMD.
VMD_HOME variable is read from the ~/.config/scipion.conf file.
"""
environ = pwutils.Environ(os.environ)
environ.set('PATH',
os.path.join(os.environ['VMD_HOME'], 'bin'),
position=pwutils.Environ.BEGIN)
return environ
def getEnviron(cls):
environ = pwutils.Environ(os.environ)
d = {}
# d['PATH'] = cls.getHome('bin')
d['PATH'] = cls.getHome('bin')
if "REMOTE_MESA_LIB" in os.environ:
d["LD_LIBRARY_PATH"] = os.environ['REMOTE_MESA_LIB']
environ.update(d, position=pwutils.Environ.BEGIN)
return environ
def getEnviron(cls):
""" Setup the environment variables needed to launch sphire. """
environ = pwutils.Environ(os.environ)
if 'PYTHONPATH' in environ:
# this is required for python virtual env to work
del environ['PYTHONPATH']
cudaLib = cls.getVar(CRYOLO_CUDA_LIB, pwem.Config.CUDA_LIB)
environ.addLibrary(cudaLib)
return environ
def getEnviron(cls):
""" Setup the environment variables needed to launch resmap. """
environ = pwutils.Environ(os.environ)
environ.update({
'PATH': Plugin.getHome(),
'LD_LIBRARY_PATH': str.join(cls.getHome(), 'locscalelib')
+ ":" + cls.getHome(),
}, position=pwutils.Environ.BEGIN)
return environ
def getEnviron(cls):
""" Return the proper environ to launch chimera.
CHIMERA_HOME variable is read from the ~/.config/scipion.conf file.
"""
environ = pwutils.Environ(os.environ)
environ.set('PATH', os.path.join(cls.getHome(), 'bin'),
position=pwutils.Environ.BEGIN)
if "REMOTE_MESA_LIB" in os.environ:
environ.set('LD_LIBRARY_PATH', os.environ['REMOTE_MESA_LIB'],
position=pwutils.Environ.BEGIN)
return environ
def getEnviron(cls):
""" Create the needed environment for Spring programs. """
environ = pwutils.Environ(os.environ)
pos = pwutils.Environ.BEGIN
environ.update(
{
'PATH':
Plugin.getHome(),
'LD_LIBRARY_PATH':
str.join(cls.getHome(), 'simple') + ':' + cls.getHome(),
},
position=pos)
return environ
def getEnviron(cls, ccpemFirst=True):
""" Create the needed environment for Xmipp programs. """
environ = pwutils.Environ(os.environ)
pos = pwutils.Environ.BEGIN if ccpemFirst else pwutils.Environ.END
environ.update(
{
'PATH': cls.getHome('bin'),
'CLIB': cls.getHome('lib'),
'CLIBD': cls.getHome('lib/data'),
'CLIBDMON': cls.getHome('lib/data/monomers'),
},
position=pos)
return environ
def getMatlabEnviron(cls, *toolPaths):
""" Return an Environment prepared for launching Matlab
scripts using the Xmipp binding.
"""
env = pwutils.Environ(os.environ)
env.set('PATH', os.environ.get('MATLAB_BINDIR', ''), pwutils.Environ.BEGIN)
env.set('LD_LIBRARY_PATH', os.environ.get('MATLAB_LIBDIR', ''),
pwutils.Environ.BEGIN)
for toolpath in toolPaths:
env.set('MATLABPATH', toolpath, pwutils.Environ.BEGIN)
env.set('MATLABPATH', os.path.join(os.environ[XMIPP_HOME],
'libraries', 'bindings', 'matlab'),
pwutils.Environ.BEGIN)
return env
def getEnviron(cls):
""" Return the environ settings to run Simple programs. """
environ = pwutils.Environ(os.environ)
SIMPLEBIN = cls.getHome('bin')
environ.update(
{
'SIMPLEBIN': SIMPLEBIN,
'SIMPLEPATH': cls.getHome(),
'SIMPLESYS': cls.getHome(),
'PATH': SIMPLEBIN + os.pathsep + cls.getHome('apps')
},
position=pwutils.Environ.BEGIN)
return environ
def getEnviron(cls):
""" Return the environ settings to run Simple programs. """
environ = pwutils.Environ(os.environ)
SIMPLEBIN = cls.getHome('build/bin')
SIMPLEPATH = cls.getHome('build')
PATH = '${' + SIMPLEPATH + '}/scripts:${' + SIMPLEPATH + '}/bin:${PATH}'
environ.update(
{
'SIMPLEBIN': SIMPLEBIN,
'SIMPLEPATH': SIMPLEPATH,
'SIMPLESYS': SIMPLEPATH,
'PATH': PATH,
},
position=pwutils.Environ.BEGIN)
return environ
def getRelionEnviron(cls):
""" Setup the environment variables needed to launch Relion. """
environ = pwutils.Environ(os.environ)
binPath = cls.__getRelionHome('bin')
libPath = cls.__getRelionHome('lib') + ":" + cls.__getRelionHome('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=pwutils.Environ.BEGIN)
# Take Scipion CUDA library path
cudaLib = environ.getFirst(('RELION_CUDA_LIB', 'CUDA_LIB'))
environ.addLibrary(cudaLib)
return environ
def getEnviron(cls, schrodingerFirst=True):
""" Create the needed environment for Schrodinger programs. """
environ = pwutils.Environ(os.environ)
pos = pwutils.Environ.BEGIN if schrodingerFirst else pwutils.Environ.END
environ.update(
{
'SCHRODINGER':
cls.getHome(''),
'PATH':
cls.getHome(''),
'LD_LIBRARY_PATH':
cls.getMMshareDir('lib/Linux-x86_64') + ':' +
cls.getHome('internal/lib'),
'PYTHONPATH':
cls.getSitePackages()
},
position=pos)
return environ
def getEnviron(cls, xmippFirst=True):
""" Create the needed environment for Xmipp programs. """
environ = pwutils.Environ(os.environ)
pos = pwutils.Environ.BEGIN if xmippFirst else pwutils.Environ.END
environ.update(
{
'PATH': getXmippPath('bin'),
'LD_LIBRARY_PATH': getXmippPath('lib'),
'PYTHONPATH': getXmippPath('pylib')
},
position=pos)
# environ variables are strings not booleans
if os.environ.get('CUDA', 'False') != 'False':
environ.update(
{
'PATH': os.environ.get('CUDA_BIN', ''),
'LD_LIBRARY_PATH': os.environ.get('NVCC_LIBDIR', '')
},
position=pos)
return environ
def getEnviron(cls):
""" Setup the environment variables needed to launch Eman. """
environ = pwutils.Environ(os.environ)
pathList = [cls.getHome(d) for d in ['lib', 'bin']]
# 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': cls.getHome('bin')},
position=pwutils.Environ.BEGIN)
environ.update(
{
'LD_LIBRARY_PATH': os.pathsep.join(pathList),
'PYTHONPATH': os.pathsep.join(pathList),
'SCIPION_MPI_FLAGS': os.environ.get('EMANMPIOPTS', ''),
'TF_FORCE_GPU_ALLOW_GROWTH': 'true'
},
position=pwutils.Environ.REPLACE)
return environ
def getEnviron(cls, first=True):
def deleteEnv(name):
if name in os.environ:
os.environ.pop(name)
environ = pwutils.Environ(os.environ)
#environ = pwutils.Environ()
# pos = pwutils.Environ.BEGIN if ccp4First else pwutils.Environ.END
_ccp4_home = cls.getHome()
_ccp4_master, _dir = os.path.split(_ccp4_home)
_username = getpass.getuser()
deleteEnv("CCP4_MASTER")
environ.update({
'PATH': Plugin.getHome(),
'LD_LIBRARY_PATH': str.join(cls.getHome(), 'lib')
+ ":" + cls.getHome(),
}, position=pwutils.Environ.BEGIN) # add to variable
environ.update({
# # CCP4_MASTER is the location of the top-level directory
# # containing ccp4-N.N.N.
# export CCP4_MASTER=/home/roberto
# export CCP4=$CCP4_MASTER/ccp4-6.5
# alias xtal='pushd $CCP4_MASTER>/dev/null'
'CCP4_MASTER': _ccp4_master,
# alias ccp4='pushd $CCP4>/dev/null'
'CCP4': _ccp4_home,
# # CCP4_SCR: a per-user directory for run-time-generated scratch
# # files.
# export CCP4_SCR=/tmp/`whoami`
'CCP4_SCR': os.path.join("/tmp", _username),
# # This variable is set to ensure that the logfile output from programs
# # compiled with Gfortran is in the correct order.
# export GFORTRAN_UNBUFFERED_PRECONNECTED=Y
'GFORTRAN_UNBUFFERED_PRECONNECTED': "Y",
# # CBIN: location of the executables -- must be on your path
# # (see below)
# export CBIN=$CCP4/bin
# alias cbin='pushd $CBIN>/dev/null'
'CBIN': os.path.join(_ccp4_home, 'bin'),
# # CLIB: location of (binary) library files such as libccp4.a
# # and libccp4.so
# export CLIB=$CCP4/lib
# alias clib='pushd $CLIB>/dev/null'
'CLIB': os.path.join(_ccp4_home, 'lib'),
# # CLIBD: platform-independent data files
# export CLIBD=$CCP4/lib/data
# alias clibd='pushd $CLIBD>/dev/null'
'CLIBD': os.path.join(_ccp4_home, 'lib', 'data'),
# # CETC: executable scripts (NOT configuration files)
# export CETC=$CCP4/etc
# alias cetc='pushd $CETC>/dev/null'
'CETC': os.path.join(_ccp4_home, 'etc'),
# # CINCL: headers and two *.def files for handling
# # "logical names" in CCP4
# export CINCL=$CCP4/include
# alias cincl='pushd $CINCL>/dev/null'
'CINCL': os.path.join(_ccp4_home, 'include'),
# # CHTML: html documentation
# export CHTML=$CCP4/html
# alias chtml='pushd $CHTML>/dev/null'
'CHTML': os.path.join(_ccp4_home, 'html'),
# # CEXAM: examples and some tests
# export CEXAM=$CCP4/examples
# alias cexam='pushd $CEXAM>/dev/null'
'CEXAM': os.path.join(_ccp4_home, 'examples'),
# # CCP4I_TOP: the top directory of the interface
# export CCP4I_TOP=$CCP4/share/ccp4i
# # source code directories
# #export CLIBS=$CCP4/lib/libccp4
# #alias clibs='pushd $CLIBS>/dev/null'
# #export CPROG=$CCP4/src
# #alias cprog='pushd $CPROG>/dev/null'
'CCP4I_TOP': os.path.join(_ccp4_home, 'share', 'ccp4i'),
# # MMCIFDIC: platform-dependent (not in $CLIBD) data file for
# # the ccif library
# export MMCIFDIC=$CLIB/ccp4/cif_mmdic.lib
'MMCIFDIC': os.path.join(_ccp4_home, 'lib', 'cif_mmdic.lib'),
# # CLIBD_MON: dictionary files for REFMAC5 (keep trailing /)
# export CLIBD_MON=$CCP4/lib/data/monomers/
'CLIBD_MON': os.path.join(_ccp4_home, 'lib', 'data', 'monomers'),
# # CRANK: location of Crank automation suite within ccp4i
# export CRANK=$CCP4I_TOP/crank
'CRANK': os.path.join(_ccp4_home, 'crank'),
# # CCP4_HELPDIR: location of the VMS-style help file used
# # by (ip)mosflm
# export CCP4_HELPDIR=$CCP4/help/ # NB trailing /
'CCP4_HELPDIR': os.path.join(_ccp4_home, 'help'),
}, position=pwutils.Environ.REPLACE) # replace
return environ
