Source code for novactf

# **************************************************************************
# *
# * Authors:     Federico P. de Isidro Gomez (fp.deisidro@cnb.csi.es) [1]
# *
# * [1] Centro Nacional de Biotecnologia, CSIC, Spain
# *
# * 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 pwem

from .constants import NOVACTF_HOME

__version__ = '3.0.2'
_logo = ""
_references = []


[docs]class Plugin(pwem.Plugin): _homeVar = NOVACTF_HOME @classmethod def _defineVariables(cls): cls._defineEmVar(NOVACTF_HOME, 'novactf-master')
[docs] @classmethod def getEnviron(cls): return None
[docs] @classmethod def getDependencies(cls): neededPrograms = ['wget', 'unzip', 'fftw3', 'fftw3f', 'lib64', 'gcc'] return neededPrograms
[docs] @classmethod def defineBinaries(cls, env): version = 'master' NOVACTF_INSTALLED = 'novactf_%s_installed' % version warningMsg = "'WARNING: if program fails when executing reinstall in scipion3/software/em/novactf-master " \ "setting the path to the include files from fftw3 as well as following fftw3 libraries: fftw3 " \ "fftw3f. Typically both libraries should be in one folder and thus one library path should be " \ "sufficient. Example command:'" \ "'make includepath = \"path_to_fftw_include_files\" libpath = \"path_to_fftw_libraries\"'" \ "'NovaCTF also requires standard libraries with the standard path being " \ "/usr/lib64 - if the libraries are elsewhere open makefile and change the path accordingly'" # Display warning message installationCmd = 'echo %s && ' % warningMsg # Download git repo installationCmd += 'wget https://github.com/turonova/novaCTF/archive/master.zip && ' \ 'unzip master.zip && ' # Binaries compilation installationCmd += 'cd novaCTF-master && ' \ 'make && ' \ 'cd .. && ' # Create installation finished flag file installationCmd += 'touch %s ' % NOVACTF_INSTALLED env.addPackage('novactf', version=version, tar='void.tgz', neededProgs=cls.getDependencies(), commands=[(installationCmd, NOVACTF_INSTALLED)], default=True)
[docs] @classmethod def runNovactf(cls, protocol, program, args, cwd=None): """ Run NovaCTF command from a given protocol. """ fullProgram = '%s/%s/%s' % (cls.getVar(NOVACTF_HOME), "novaCTF-master", program) protocol.runJob(fullProgram, args, env=cls.getEnviron(), cwd=cwd)