# **************************************************************************
# *
# * Authors: Federico P. de Isidro Gomez (fp.deisidro@cnb.csic.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__ = '3.0.5'
_logo = ""
_references = ["Turonova2017"]
[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)