# **************************************************************************
# *
# * Authors: Grigory Sharov (gsharov@mrc-lmb.cam.ac.uk)
# *
# * MRC Laboratory of Molecular Biology (MRC-LMB)
# *
# * 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 pwem
from pyworkflow import Config
from pyworkflow.utils import Environ
from .constants import *
__version__ = '3.0.9'
_logo = "salk_logo.jpg"
_references = ['tan2017']
[docs]class Plugin(pwem.Plugin):
_homeVar = FSC3D_HOME
_pathVars = [FSC3D_HOME]
_supportedVersions = V3_0
_url = "https://github.com/scipion-em/scipion-em-fsc3d"
_condaActivationCmd = None
@classmethod
def _defineVariables(cls):
cls._defineEmVar(FSC3D_HOME, 'fsc3D-3.0')
cls._defineVar(FSC3D_ACTIVATION_CMD, 'conda activate 3DFSC')
[docs] @classmethod
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
[docs] @classmethod
def getFSCEnvActivation(cls):
activation = cls.getVar(FSC3D_ACTIVATION_CMD)
scipionHome = Config.SCIPION_HOME + os.path.sep
return activation.replace(scipionHome, "", 1)
[docs] @classmethod
def runProgram(cls, protocol, args, cwd=None):
""" Return the program binary that will be used. """
cmd = '%s %s && ' % (cls.getCondaActivationCmd(),
cls.getFSCEnvActivation())
cmd += cls.getHome('ThreeDFSC', 'ThreeDFSC_Start.py')
protocol.runJob(cmd, args, env=cls.getEnviron(), cwd=cwd)
[docs] @classmethod
def defineBinaries(cls, env):
# try to get CONDA activation command
condaActivationCmd = cls.getCondaActivationCmd()
neededProgs = []
if not condaActivationCmd:
neededProgs = ['conda']
condaActivationCmd += 'conda env create -f environment.yml &&'
fsc_commands = [(condaActivationCmd + 'touch IS_INSTALLED',
'IS_INSTALLED')]
envPath = os.environ.get('PATH', "")
# keep path since conda likely in there
installEnvVars = {'PATH': envPath} if envPath else None
env.addPackage('fsc3D', version='3.0',
url='https://github.com/azazellochg/fsc3D/archive/3.0.tar.gz',
commands=fsc_commands,
neededProgs=neededProgs,
default=True,
vars=installEnvVars)