Skip to content

Fix where singularity build ends up with empty parameter #4

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
rpetit3 merged 4 commits into from
May 20, 2026
Merged

Fix where singularity build ends up with empty parameter #4

Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
a2e44a7
Fix where singularity build ends up with empty parameter
pvanheus May 20, 2026
5d45548
Replace string split with shlex split
pvanheus May 20, 2026
4efd8ae
Return stdout and stderr even if command fails
pvanheus May 20, 2026
55c6de2
Fix and rationalise error reporting
pvanheus May 20, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
16 changes: 10 additions & 6 deletions bactopia/utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
import logging
import shlex
import subprocess
import sys
from pathlib import Path
Expand Down Expand Up @@ -33,7 +34,7 @@ def execute(
logging.debug(f"Working directory: {directory}")
try:
command = subprocess.run(
cmd.split(" "), # Replace with your command and arguments
shlex.split(cmd), # Replace with your command and arguments
cwd=directory,
capture_output=True,
text=True, # Decodes stdout/stderr as strings using default encoding
Expand All @@ -49,15 +50,18 @@ def execute(
return command.returncode
except subprocess.CalledProcessError as e:
if allow_fail:
logging.debug(f'"{cmd}" return exit code {e.returncode}')
logging.debug(e)
logger = logging.debug
else:
logger = logging.error
logger(f"STDOUT: \n{e.stdout}")
logger(f"STDERR:\n{e.stderr}")
logger(f'"{cmd}" return exit code {e.returncode}')
logger(e)
if allow_fail:
return None
else:
logging.error(f'"{cmd}" return exit code {e.returncode}')
logging.error(e)
sys.exit(e.returncode)


def pgzip(files: list, cpus: int) -> list:
"""
Parallel gzip a list of files
Expand Down
Loading