Source code for bsoft

# **************************************************************************
# *
# * 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)