# **************************************************************************
# *
# * Authors: David Maluenda (dmaluenda@cnb.csic.es)
# * Yunior C. Fonseca Reyna (cfonseca@cnb.csic.es)
# *
# * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * 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 2 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
import pyworkflow.utils as pwutils
from .constants import *
__version__ = '3.0.4'
_logo = "locscale_logo.jpg"
_references = ['Jakobi2017']
[docs]class Plugin(pwem.Plugin):
_homeVar = LOCSCALE_HOME
_pathVars = [LOCSCALE_HOME]
_supportedVersions = [V0_1]
@classmethod
def _defineVariables(cls):
cls._defineEmVar(LOCSCALE_HOME, 'locscale-0.1')
[docs] @classmethod
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
[docs] @classmethod
def isVersionActive(cls):
return cls.getActiveVersion().startswith(V0_1)
[docs] @classmethod
def getEmanPlugin(self):
# --- Eman2 dependencies ---
try:
emanPlugin = Domain.importFromPlugin("eman2", "Plugin",
doRaise=True)
emanPlugin._defineVariables()
except Exception as e:
print(pwutils.redStr("Eman plugin does not installed....You need to install it "
"first."))
return None
return emanPlugin
[docs] @classmethod
def getEmanDependencies(self):
# to set the Eman2 environ in a bash-shell
emanPlugin = self.getEmanPlugin()
EMAN_ENV_STR = ' '.join(['%s=%s' % (var, emanPlugin.getEnviron()[var])
for var in
('PATH', 'PYTHONPATH', 'LD_LIBRARY_PATH')])
return EMAN_ENV_STR
[docs] @classmethod
def defineBinaries(cls, env):
emanPlugin = cls.getEmanPlugin()
EMAN_ENV_STR = cls.getEmanDependencies()
emanmpi4piFlag = "mpi4py-installed"
env.addPackage('locscale', version='0.1',
tar='locscale-0.1.tgz',
commands=[('echo ; echo " > Installing mpi4py in eman2" && '
'export %s && pip install mpi4py && touch %s' % (EMAN_ENV_STR, emanmpi4piFlag),
emanPlugin.getHome('lib', 'python2.7', 'site-packages', 'mpi4py')),
('echo', 'source/locscale_mpi.py')],
default=True)