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