def _setup(self, config, temp):
CommandNode._setup(self, config, temp)
# The temp folder may contain old files:
# Remove old pipes to prevent failure at _teardown
for pipe_fname in glob.glob(os.path.join(temp, "pipe*")):
fileutils.try_remove(pipe_fname)
# ExaML refuses to overwrite old info files
fileutils.try_remove(os.path.join(temp, "ExaML_info.Pypeline"))
# Resume from last checkpoint, if one such was generated
checkpoints = glob.glob(
os.path.join(temp, "ExaML_binaryCheckpoint.Pypeline_*"))
if not checkpoints:
return
cache = FileStatusCache()
if cache.files_up_to_date(checkpoints, self.input_files):
checkpoints.sort(key=lambda fname: int(fname.rsplit("_", 1)[-1]))
# FIXME: Less hacky solution to modifying AtomicCmds needed
self._command._command.append("-R")
self._command._command.append(checkpoints[-1])
else:
for fpath in checkpoints:
fileutils.try_remove(fpath)
def _setup(self, config, temp):
CommandNode._setup(self, config, temp)
# The temp folder may contain old files:
# Remove old pipes to prevent failure at _teardown
for pipe_fname in glob.glob(os.path.join(temp, "pipe*")):
fileutils.try_remove(pipe_fname)
# ExaML refuses to overwrite old info files
fileutils.try_remove(os.path.join(temp, "ExaML_info.Pypeline"))
# Resume from last checkpoint, if one such was generated
checkpoints = glob.glob(os.path.join(temp,
"ExaML_binaryCheckpoint.Pypeline_*"))
if not checkpoints:
return
cache = FileStatusCache()
if cache.files_up_to_date(checkpoints, self.input_files):
checkpoints.sort(key=lambda fname: int(fname.rsplit("_", 1)[-1]))
# FIXME: Less hacky solution to modifying AtomicCmds needed
self._command._command.append("-R")
self._command._command.append(checkpoints[-1])
else:
for fpath in checkpoints:
fileutils.try_remove(fpath)
def _setup(self, config, temp):
CommandNode._setup(self, config, temp)
for fname in ("3pGtoA_freq.txt", "5pCtoT_freq.txt", "dnacomp.txt",
"misincorporation.txt"):
relpath = os.path.join(self._directory, fname)
abspath = os.path.abspath(relpath)
os.symlink(abspath, os.path.join(temp, fname))
def _setup(self, config, temp):
"""See CommandNode._setup."""
infile = os.path.abspath(self._infile)
outfile = reroot_path(temp, self._infile)
os.symlink(infile, outfile)
CommandNode._setup(self, config, temp)
def _setup(self, config, temp):
if self._check_fastqs:
check_fastq_files(self.input_files, self._quality_offset)
os.mkfifo(os.path.join(temp, self._basename + ".discarded"))
os.mkfifo(os.path.join(temp, self._basename + ".pair1.truncated"))
os.mkfifo(os.path.join(temp, self._basename + ".pair2.truncated"))
os.mkfifo(os.path.join(temp, "uncompressed_input_1"))
os.mkfifo(os.path.join(temp, "uncompressed_input_2"))
if self._version == VERSION_15:
if self._collapse:
os.mkfifo(os.path.join(temp, self._basename + ".collapsed"))
os.mkfifo(
os.path.join(temp,
self._basename + ".collapsed.truncated"))
os.mkfifo(
os.path.join(temp, self._basename + ".singleton.truncated"))
else:
os.mkfifo(
os.path.join(temp,
self._basename + ".singleton.aln.truncated"))
os.mkfifo(
os.path.join(temp,
self._basename + ".singleton.unaln.truncated"))
CommandNode._setup(self, config, temp)
def _setup(self, config, temp):
CommandNode._setup(self, config, temp)
for fname in ("3pGtoA_freq.txt", "5pCtoT_freq.txt", "dnacomp.txt",
"misincorporation.txt"):
relpath = os.path.join(self._directory, fname)
abspath = os.path.abspath(relpath)
os.symlink(abspath, os.path.join(temp, fname))
def _setup(self, config, temp):
for key in ("IN_ALIGNMENT", "IN_PARTITION"):
source = os.path.abspath(self._kwargs[key])
destination = os.path.join(temp, self._kwargs["TEMP_" + key])
os.symlink(source, destination)
CommandNode._setup(self, config, temp)
def _setup(self, config, temp):
for key in ("IN_ALIGNMENT", "IN_PARTITION"):
source = self._kwargs[key]
destination = os.path.join(temp, self._kwargs["TEMP_" + key])
fileutils.copy_file(source, destination)
CommandNode._setup(self, config, temp)
def _setup(self, config, temp):
for key in ("IN_ALIGNMENT", "IN_PARTITION"):
source = self._kwargs[key]
destination = os.path.join(temp, self._kwargs["TEMP_" + key])
fileutils.copy_file(source, destination)
CommandNode._setup(self, config, temp)
def _setup(self, config, temp):
check_fastq_files(self.input_files, self._quality_offset)
os.mkfifo(os.path.join(temp, self._basename + ".truncated"))
os.mkfifo(os.path.join(temp, self._basename + ".discarded"))
os.mkfifo(os.path.join(temp, "uncompressed_input"))
CommandNode._setup(self, config, temp)
def _setup(self, config, temp):
check_fastq_files(self.input_files, self._quality_offset)
os.mkfifo(os.path.join(temp, self._basename + ".truncated"))
os.mkfifo(os.path.join(temp, self._basename + ".discarded"))
os.mkfifo(os.path.join(temp, "uncompressed_input"))
CommandNode._setup(self, config, temp)
def _setup(self, config, temp):
for key in ("IN_ALIGNMENT", "IN_PARTITION"):
source = os.path.abspath(self._kwargs[key])
destination = os.path.join(temp, self._kwargs["TEMP_" + key])
os.symlink(source, destination)
CommandNode._setup(self, config, temp)
def _setup(self, config, temp):
CommandNode._setup(self, config, temp)
# Required to avoid the creation of files outside the temp folder
for filename in self._symlinks:
source = os.path.abspath(filename)
destination = os.path.join(temp, os.path.basename(filename))
os.symlink(source, destination)
def _setup(self, config, temp):
CommandNode._setup(self, config, temp)
# Required to avoid the creation of files outside the temp folder
for filename in self._symlinks:
source = os.path.abspath(filename)
destination = os.path.join(temp, os.path.basename(filename))
os.symlink(source, destination)
def _setup(self, config, temp_root):
CommandNode._setup(self, config, temp_root)
dst_fname = os.path.join(temp_root, self._bam_input.pipe)
if len(self._bam_input.files) > 1:
os.mkfifo(dst_fname)
else:
src_fname, = self._bam_input.files
os.symlink(os.path.join(os.getcwd(), src_fname), dst_fname)
src_fname = os.path.join(os.getcwd(), swap_ext(src_fname, ".bai"))
os.symlink(src_fname, dst_fname + ".bai")
def _setup(self, config, temp_root):
CommandNode._setup(self, config, temp_root)
dst_fname = os.path.join(temp_root, self._bam_input.pipe)
if len(self._bam_input.files) > 1:
os.mkfifo(dst_fname)
else:
src_fname, = self._bam_input.files
os.symlink(os.path.join(os.getcwd(), src_fname), dst_fname)
src_fname = os.path.join(os.getcwd(), swap_ext(src_fname, ".bai"))
os.symlink(src_fname, dst_fname + ".bai")
def _setup(self, config, temp):
os.mkfifo(os.path.join(temp, self._basename + ".discarded"))
os.mkfifo(os.path.join(temp, self._basename + ".pair1.truncated"))
os.mkfifo(os.path.join(temp, self._basename + ".pair2.truncated"))
os.mkfifo(os.path.join(temp, "uncompressed_input_1"))
os.mkfifo(os.path.join(temp, "uncompressed_input_2"))
if self._version == VERSION_15:
os.mkfifo(os.path.join(temp, self._basename + ".collapsed"))
os.mkfifo(os.path.join(temp, self._basename + ".collapsed.truncated"))
os.mkfifo(os.path.join(temp, self._basename + ".singleton.truncated"))
else:
os.mkfifo(os.path.join(temp, self._basename + ".singleton.aln.truncated"))
os.mkfifo(os.path.join(temp, self._basename + ".singleton.unaln.truncated"))
CommandNode._setup(self, config, temp)
def _do_test_commandnode_setup(kwargs):
cmd_mock = _build_cmd_mock(**kwargs)
node = CommandNode(cmd_mock)
node._setup(None, None)
def _setup(self, config, temp):
CommandNode._setup(self, config, temp)
os.mkfifo(os.path.join(temp, self._basename))
def _setup(self, config, temp):
CommandNode._setup(self, config, temp)
os.mkfifo(os.path.join(temp, self._basename))
def _setup(self, config, temp):
os.symlink(os.path.abspath(self._input_alignment),
os.path.join(temp, "RAxML_alignment"))
os.symlink(os.path.abspath(self._input_partitions),
os.path.join(temp, "RAxML_partitions"))
CommandNode._setup(self, config, temp)
def _setup(self, config, temp):
os.mkfifo(os.path.join(temp, self._basename + ".truncated"))
os.mkfifo(os.path.join(temp, self._basename + ".discarded"))
os.mkfifo(os.path.join(temp, "uncompressed_input"))
CommandNode._setup(self, config, temp)
def _setup(self, config, temp):
os.mkfifo(os.path.join(temp, self._basename + ".truncated"))
os.mkfifo(os.path.join(temp, self._basename + ".discarded"))
os.mkfifo(os.path.join(temp, "uncompressed_input"))
CommandNode._setup(self, config, temp)
def _do_test_commandnode_setup(kwargs):
cmd_mock = _build_cmd_mock(**kwargs)
node = CommandNode(cmd_mock)
node._setup(None, None)
def _setup(self, config, temp):
os.symlink(os.path.abspath(self._input_alignment), os.path.join(temp, "RAxML_alignment"))
os.symlink(os.path.abspath(self._input_partitions), os.path.join(temp, "RAxML_partitions"))
CommandNode._setup(self, config, temp)