# **************************************************************************
# *
# * Authors: J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [1]
# *
# * [1] SciLifeLab, Stockholm University
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 3 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************
import os
import pyworkflow.utils as pwutils
import pwem
from .constants import *
__version__ = '3.1.3'
_logo = "relion_logo.jpg"
_references = ['Scheres2012a', 'Scheres2012b', 'Kimanius2016', 'Zivanov2018']
[docs]class Plugin(pwem.Plugin):
_homeVar = RELION_HOME
_supportedVersions = [V3_1_0, V3_1_1, V3_1_2]
_url = "https://github.com/scipion-em/scipion-em-relion"
@classmethod
def _defineVariables(cls):
cls._defineEmVar(RELION_HOME, 'relion-%s' % V3_1_2)
cls._defineVar(RELION_CUDA_LIB, pwem.Config.CUDA_LIB)
[docs] @classmethod
def getEnviron(cls):
""" Setup the environment variables needed to launch Relion. """
environ = pwutils.Environ(os.environ)
binPath = os.pathsep.join([cls.getHome('bin'),
pwem.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=pwutils.Environ.BEGIN)
# Get Relion CUDA library path if defined
cudaLib = cls.getVar(RELION_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=pwutils.Environ.BEGIN)
return environ
[docs] @classmethod
def IS_GT31(cls):
return not cls.getActiveVersion().startswith('3.1')
[docs] @classmethod
def defineBinaries(cls, env):
relion_commands = [('cmake -DGUI=OFF -DCMAKE_INSTALL_PREFIX=./ .', []),
('make -j %d' % env.getProcessors(),
['bin/relion_refine'])]
for v in cls._supportedVersions:
env.addPackage('relion', version=v,
url='https://github.com/3dem/relion/archive/%s.tar.gz' % v,
commands=relion_commands,
updateCuda=True,
default=v == V3_1_2)