Source code for deepfinder

# **************************************************************************
# *
# * Authors:     you (you@yourinstitution.email)
# *
# * your institution
# *
# * 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'
# *
# **************************************************************************
from os.path import join

import pwem

from .constants import *

_logo = "icon.png"
_references = ['EMMANUEL2020']

[docs]class Plugin(pwem.Plugin): _homeVar = DF_HOME _pathVars = [DF_HOME] @classmethod def _defineVariables(cls): cls._defineEmVar(DF_HOME, DF_FOLDER + '-' + DF_VERSION) cls._defineVar(DF_ENV_ACTIVATION, DEFAULT_ACTIVATION_CMD)
[docs] @classmethod def getEnviron(cls): pass
[docs] @classmethod def getDeepFinderEnvActivation(cls): return cls.getVar(DF_ENV_ACTIVATION)
[docs] @classmethod def runDeepFinder(cls, protocol, program, args, cwd=None): program = cls.getDeepFinderProgram(program) fullProgram = '%s %s && %s' % (cls.getCondaActivationCmd(), cls.getDeepFinderEnvActivation(), program) protocol.runJob(fullProgram, args, env=cls.getEnviron(), cwd=cwd)
[docs] @classmethod def getDeepFinderProgram(cls, program): return os.path.join(cls.getHome(), 'bin', '%s' % program)
[docs] @classmethod def getDependencies(cls): neededProgs = [] condaActivationCmd = cls.getCondaActivationCmd() if not condaActivationCmd: neededProgs.append('conda') return neededProgs
[docs] @classmethod def defineBinaries(cls, env): cls.addDeepFinderPackage(env, DF_VERSION)
[docs] @classmethod def addDeepFinderPackage(cls, env, version): DF_INSTALLED = 'deepfinder_%s_installed' % version env_name = getDFEnvName(version) # try to get CONDA activation command installationCmd = cls.getCondaActivationCmd() # Create the environment installationCmd += 'conda create -y -n %s -c anaconda python=3.6 && ' \ % env_name # Activate new the environment installationCmd += 'conda activate %s && ' % env_name # Install downloaded code installationCmd += 'pip install -r requirements.txt && ' # for GPU usage should be requirements_gpu.txt # Flag installation finished installationCmd += 'touch %s' % DF_INSTALLED df_commands = [(installationCmd, DF_INSTALLED)] env.addPackage(DF_FOLDER, version=version, url='https://gitlab.inria.fr/serpico/deep-finder/-/archive/master/deep-finder-master.tar.gz', commands=df_commands, buildDir='deep-finder-master', neededProgs=cls.getDependencies(), default=True)
[docs] @classmethod def getDeepFinderCmd(cls, program): """ Composes a DeepFinder command for a given program. """ # Program to run program = cls.getDeepFinderProgram(program) fullProgram = '%s %s && %s' % (cls.getCondaActivationCmd(), cls.getDeepFinderEnvActivation(), program) # Command to run cmd = fullProgram return cmd