def __init__(self, scheduler, projectId):
self.checkScheduler(scheduler)
self.scheduler = scheduler # SGE
self.projectId = projectId
self.groupId2group = {} # key=identifier value=object
self.path2db = "%s/%s_%s.db" % (os.getcwd(), self.projectId,
Utils.uniq_alphanum(5))
self.db = DbSqlite(self.path2db)
self.setUpJobTable()
def getVersionGatk(pathToJar=None):
if pathToJar == None:
pathToJar = Utils.getProgramPath("GenomeAnalysisTK.jar")
args = ["java", "-Xmx1g", "-jar", pathToJar, "--version"]
# p = subprocess.Popen(args, shell=True, stdout=subprocess.PIPE).communicate()
cmd = " ".join(args)
p = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE).communicate()
version = p[0].split("-")[0]
majVer = int(version.split(".")[0])
minVer = int(version.split(".")[1])
return majVer, minVer