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): 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): 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): 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): 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): 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)