# **************************************************************************
# *
# * Authors: J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se)
# *
# * 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 pwem
from pyworkflow.utils import Environ
from bsoft.constants import BSOFT_HOME, V2_0_7, V1_9_0, BSOFT
__version__ = '3.0.5'
_logo = "bsoft_logo.png"
_references = ['Heymann2007', 'Heymann2018']
[docs]class Plugin(pwem.Plugin):
_homeVar = BSOFT_HOME
_pathVars = [BSOFT_HOME]
_supportedVersions = [V2_0_7]
@classmethod
def _defineVariables(cls):
cls._defineEmVar(BSOFT_HOME, BSOFT + "-" + V2_0_7)
[docs] @classmethod
def getEnviron(cls, bsoftVersion=None):
""" Setup the environment variables needed to launch bsoft.
:param bsoftVersion (optional) pass a version to be used,
otherwise will choose default value for BSOFT_HOME"""
environ = Environ(os.environ)
home = cls.getHomeFromVersion(bsoftVersion)
environ.update({
'PATH': os.path.join(home, 'bin'),
'BSOFT': home
}, position=Environ.BEGIN)
return environ
[docs] @classmethod
def getHomeFromVersion(self, bsoftVersion):
return Plugin.getHome() if bsoftVersion is None else os.path.join(pwem.Config.EM_ROOT, BSOFT + "-" + bsoftVersion)
[docs] @classmethod
def getProgram(cls, program, bsoftVersion=None):
""" Return the program binary that will be used. """
return os.path.join(cls.getHomeFromVersion(bsoftVersion),"bin", program)
[docs] @classmethod
def defineBinaries(cls, env):
env.addPackage(BSOFT, version='1.9.0',
tar='bsoft1_9_0_Fedora_20.tgz',
default=True)
env.addPackage(BSOFT, version='2.0.7',
url="https://lsbr.niams.nih.gov/bsoft/bsoft2_0_7_CentOS_7.7.1908.tgz",
buildDir = "bsoft",
default=True)