# **************************************************************************
# *
# * Authors: J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se)
# *
# * 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 .constants import *
__version__ = '3.1.5'
_logo = "spider_logo.png"
_references = ['Shaikh2008', 'Frank1996b']
[docs]class Plugin(pwem.Plugin):
_homeVar = SPIDER_HOME
_pathVars = [SPIDER_HOME]
_supportedVersions = ['26.06']
_url = "https://github.com/scipion-em/scipion-em-spider"
@classmethod
def _defineVariables(cls):
cls._defineEmVar(SPIDER_HOME, 'spider-26.06')
cls._defineVar(SPIDER, 'spider_linux_mp_intel64')
cls._defineVar(SPIDER_MPI, 'spider_linux_mpi_opt64')
[docs] @classmethod
def getEnviron(cls):
""" Load the environment variables needed for Spider.
If SPIDER_HOME is defined, the bin, man and proc folders will be
defined from it. If not, each of them should be defined separately.
"""
env = Environ(os.environ)
if cls.getHome():
env.update( # Spider needs this extra slash at the end
{SPBIN_DIR: cls.getHome('spider/bin') + '/',
SPMAN_DIR: cls.getHome('spider/man') + '/',
SPPROC_DIR: cls.getHome('spider/proc') + '/'})
else:
errors = ''
for var in [SPBIN_DIR, SPMAN_DIR, SPPROC_DIR]:
if var not in env:
errors += "\n Missing SPIDER variable: '%s'" % var
if len(errors):
print("ERRORS: " + errors)
env.set('PATH', env[SPBIN_DIR], env.END)
return env
[docs] @classmethod
def getScript(cls, *paths):
""" Return the script that will be used. """
cmd = os.path.join(__path__[0], 'scripts', cls.getActiveVersion(), *paths)
return str(cmd)
[docs] @classmethod
def getProgram(cls, mpi=False):
if mpi:
program = os.path.basename(cls.getVar(SPIDER_MPI))
else:
program = os.path.basename(cls.getVar(SPIDER))
cmd = os.path.abspath(os.path.join(cls.getEnviron()[SPBIN_DIR], program))
return str(cmd)
[docs] @classmethod
def defineBinaries(cls, env):
env.addPackage('spider', version='26.06',
url='https://github.com/spider-em/SPIDER/releases/'
'download/v26.06/spiderweb.26.06.tar.gz',
createBuildDir=True,
buildDir='spider',
target="spider/spider",
neededProgs=['csh'],
default=True)