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feat: Conda support for HTSinfer workflow #87

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Feb 11, 2024
Merged

feat: Conda support for HTSinfer workflow #87

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30 changes: 1 addition & 29 deletions zarp/snakemake/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -65,35 +65,7 @@ def compile_command(self, snakefile: Path) -> List[str]:
bind_paths_str: List[str]
bind_paths_arg: str
if self.run_config.dependency_embedding == "CONDA":
# Conda is currently not supported for the HTSinfer workflow
if snakefile.name == "htsinfer.smk":
cmd_ls.append("--use-singularity")
bind_paths = [
self.exec_dir,
self.run_config.working_directory,
self.run_config.zarp_directory,
os.environ.get("TMP"),
os.environ.get("TMPDIR"),
]
bind_paths_str = list(
set(str(item) for item in bind_paths if item is not None)
)
if self.bind_paths is not None:
bind_paths_str.extend(
[str(path) for path in self.bind_paths]
)
bind_paths_str = [
item for item in bind_paths_str if item != DUMMY_DATA
]
bind_paths_arg = ",".join(bind_paths_str)
cmd_ls.extend(
["--singularity-args", f"--bind {bind_paths_arg}"])
LOGGER.warning(
"Conda not supported for HTSinfer workflow."
" Using Singularity instead."
)
else:
cmd_ls.append("--use-conda")
cmd_ls.append("--use-conda")
elif self.run_config.dependency_embedding == "SINGULARITY":
cmd_ls.append("--use-singularity")
bind_paths = [
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