# **************************************************************************
# *
# * Authors: J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [1]
# *
# * [1] 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 subprocess
import pwem
import pyworkflow.utils as pwutils
from .constants import EMAN2_HOME, EMAN2SCRATCHDIR, V2_9, V2_31, V2_91
__version__ = '3.3.3'
_logo = "eman2_logo.png"
_references = ['Tang2007']
[docs]class Plugin(pwem.Plugin):
_homeVar = EMAN2_HOME
_pathVars = [EMAN2_HOME]
_supportedVersions = [V2_31, V2_9, V2_91]
_url = "https://github.com/scipion-em/scipion-em-eman2"
@classmethod
def _defineVariables(cls):
cls._defineEmVar(EMAN2_HOME, 'eman-' + V2_91)
cls._defineVar(EMAN2SCRATCHDIR, '/tmp')
[docs] @classmethod
def getEnviron(cls):
""" Setup the environment variables needed to launch Eman. """
environ = pwutils.Environ(os.environ)
environ.update({'PATH': cls.getHome('bin')},
position=pwutils.Environ.BEGIN)
return environ
[docs] @classmethod
def isVersion(cls, version='2.91'):
return cls.getActiveVersion() == version
[docs] @classmethod
def getActiveVersion(cls, home=None, versions=None):
""" Reimplemented here, assumes EMAN2_HOME = eman-xxx """
ver = os.path.basename(cls.getHome()).split("-")[-1]
versions = cls.getSupportedVersions()
for v in versions:
if v == ver:
return v
return ''
[docs] @classmethod
def getProgram(cls, program, python=False):
""" Return the program binary that will be used. """
program = os.path.join(cls.getHome('bin'), program)
if python:
python = cls.getHome('bin/python')
return '%(python)s %(program)s ' % locals()
else:
return '%(program)s ' % locals()
[docs] @classmethod
def getEmanCommand(cls, program, args, python=False):
return cls.getProgram(program, python) + args
[docs] @classmethod
def createEmanProcess(cls, script='e2converter.py', args=None, direc="."):
""" Open a new Process with all EMAN environment (python...etc)
that will serve as an adaptor to use EMAN library
"""
program = os.path.join(__path__[0], script)
cmd = cls.getEmanCommand(program, args, python=True)
print("** Running: '%s'" % cmd)
cmd = cmd.split()
proc = subprocess.Popen(cmd, env=cls.getEnviron(),
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
cwd=direc,
universal_newlines=True)
return proc
[docs] @classmethod
def defineBinaries(cls, env):
SW_EM = env.getEmFolder()
shell = os.environ.get("SHELL", "bash")
urls = ['https://cryoem.bcm.edu/cryoem/static/software/release-2.31/eman2.31_sphire1.3.linux64.sh',
'https://cryoem.bcm.edu/cryoem/static/software/release-2.9/eman2.9_sphire1.4_sparx.linux64.sh',
'https://cryoem.bcm.edu/cryoem/static/software/release-2.91/eman2.91_sphire1.4_sparx.linux64.sh']
for ver, url in zip(cls._supportedVersions, urls):
install_cmd = 'cd %s && wget %s && ' % (SW_EM, url)
install_cmd += '%s ./%s -b -f -p "%s/eman-%s"' % (shell, url.split('/')[-1], SW_EM, ver)
eman_commands = [(install_cmd, '%s/eman-%s/bin/python' % (SW_EM, ver))]
env.addPackage('eman', version=ver,
tar='void.tgz',
commands=eman_commands, default=ver == V2_91)