Source code for relion

# **************************************************************************
# *
# * 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__ = '4.0b1'
_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, V3_1_3, V4_0] _url = "https://github.com/scipion-em/scipion-em-relion" @classmethod def _defineVariables(cls): cls._defineEmVar(RELION_HOME, 'relion-%s' % V4_0) cls._defineVar(RELION_CUDA_LIB, pwem.Config.CUDA_LIB) cls._defineVar(RELION_PYTHON, None)
[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 cls.getActiveVersion().startswith('4')
[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 == V4_0)