Source code for resmap

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (jmdelarosa@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 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 resmap.constants import *

__version__ = '3.0.2'
_logo = "resmap_logo.png"
_references = ['kucukelbir2014']


[docs]class Plugin(pwem.Plugin): _homeVar = RESMAP_HOME _pathVars = [RESMAP_HOME] @classmethod def _defineVariables(cls): cls._defineEmVar(RESMAP_HOME, 'resmap-1.95') cls._defineVar(RESMAP, 'ResMap-1.95-cuda-Centos7x64') cls._defineVar(RESMAP_GPU_LIB, 'ResMap_krnl-cuda-V8.0.61-sm60_gpu.so')
[docs] @classmethod def getEnviron(cls): """ Setup the environment variables needed to launch resmap. """ environ = Environ(os.environ) environ.update({'PATH': Plugin.getHome()}, position=Environ.BEGIN) return environ
[docs] @classmethod def getProgram(cls): """ Return the program binary that will be used. """ return os.path.join(cls.getHome('bin'), os.path.basename(cls.getVar(RESMAP)))
[docs] @classmethod def getGpuLib(cls): """ Return CUDA lib linked to binary. """ return os.path.join(cls.getHome('bin'), os.path.basename(cls.getVar(RESMAP_GPU_LIB)))
[docs] @classmethod def defineBinaries(cls, env): """ Define required binaries in the given Environment. """ env.addPackage('resmap', version='1.95', tar='resmap-1.95.tgz', default=True)