def download_singularity_image(outfile,
container_path,
md5value=None,
force=False):
assert outfile.endswith(".simg"), "output filename must be .simg"
# download singularity
from bioconvert import configuration as config
# note that in singularity v2.4, whatever extension you put, it is
# replaced by simg
singfile = "{}/{}".format(config.user_config_dir, outfile)
if exists(singfile) and md5value and md5(
singfile) == md5value and force is False:
print("Found singularity (graphviz) image")
elif exists(singfile) and md5value is None and force is False:
print("Found singularity (graphviz) image but md5 not checked")
else:
print("Downloading singularity. Please wait")
cmd = "singularity pull --name {} {}"
if force is True:
cmd += " -F "
cmd = cmd.format(singfile, container_path)
print(cmd)
try:
from bioconvert.core.shell import shell
shell(cmd)
except:
import os
os.system(cmd)
return singfile
def shell(self, cmd):
from bioconvert.core.shell import shell
t1 = time.time()
_log.info("{}> ".format(self.name))
_log.info("CMD: {}".format(cmd))
shell(cmd)
t2 = time.time()
self.last_duration = t2 - t1
_log.info("Took {} seconds ".format(t2 - t1))
self._last_time = t2 - t1
def shell(self, cmd):
from bioconvert.core.shell import shell
_log.info("CMD: {}".format(cmd))
shell(cmd)
def test_shell():
shell("ls")