def __init__(self):
self.server = myos.which_server()
if self.server == 'broad':
self.igv_fn = '/home/unix/dfernand/bin/IGVTools/igvtools.jar'
elif self.server == 'slurm' or self.server == 'legacy':
self.dep_cmd = myos.load_dependencies_cmd(['bio/igvtools-2.2.2'])
self.igv_fn = '/n/sw/igvtools-2.2.2/igvtools.jar'
def __init__(self):
self.server = myos.which_server()
if self.server == 'broad':
self.igv_fn = '/home/unix/dfernand/bin/IGVTools/igvtools.jar'
elif self.server == 'slurm' or self.server == 'legacy':
self.dep_cmd = myos.load_dependencies_cmd(['bio/igvtools-2.2.2'])
self.igv_fn = '/n/sw/igvtools-2.2.2/igvtools.jar'
def run_fastqc(doe_csv_fn, out_dir, logs_dir, header_name_of_in_fn, extension_name, in_dir, execute):
myos.check_if_directory_exists_create_it(out_dir)
qname = 'regevlab'
mem_usage = '5000'
if extension_name is not None:
dict_fq_fns = doe_reader.create_experiment_fns(doe_csv_fn, 'name', in_dir, extension_name)
elif header_name_of_in_fn is not None:
dict_fq_fns = doe_reader.read_experiment_field(doe_csv_fn, 'name', header_name_of_in_fn)
out_dir = out_dir
dep_cmd = myos.load_dependencies_cmd(dependencies_list)
for exp_name, in_fn in dict_fq_fns.iteritems():
bsubcmd = myos.create_bsub_string_no_rm_logs_dir(logs_dir, exp_name, qname = qname, mem_usage = mem_usage)
runcmd = execs_commands.fastqc(in_fn, out_dir)
fullcmd = bsubcmd+'\"'+runcmd+'\"'
print fullcmd
if execute:
os.system(fullcmd)
return 0
def __init__(self):
self.server = myos.which_server()
if self.server == 'broad':
self.dep_cmd = myos.load_dependencies_cmd(['.bedops-2.0.0b'])
elif self.server == 'slurm' or self.server == 'legacy':
self.dep_cmd = myos.load_dependencies_cmd(['centos6/bedops-2.3.0'])
def __init__(self):
self.server = myos.which_server()
if self.server == 'broad':
self.dep_cmd = myos.load_dependencies_cmd(['.bedops-2.0.0b'])
elif self.server == 'slurm' or self.server == 'legacy':
self.dep_cmd = myos.load_dependencies_cmd(['centos6/bedops-2.3.0'])
