Set up sentry #68
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Set up sentry #68
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luizirber
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Jun 26, 2024
The shell execution code changed in #68, `snakemake.shell` was replaced with `subprocess.run`. This broke the NCBI assemblies processing, and investigation led to the conclusion it was because `snakemake.shell` defaults to `/bin/bash` for the shell, while `subprocess.run` uses `/bin/sh`, and the assembly task uses a `bash` redirect that is a syntax error for `sh`. Also fix the shell quoting, since `{:q}` is `snakemake`-specific.
luizirber
added a commit
that referenced
this pull request
Jul 23, 2024
The shell execution code changed in #68, `snakemake.shell` was replaced with `subprocess.run`. This broke the NCBI assemblies processing, and investigation led to the conclusion it was because `snakemake.shell` defaults to `/bin/bash` for the shell, while `subprocess.run` uses `/bin/sh`, and the assembly task uses a `bash` redirect that is a syntax error for `sh`. Also fix the shell quoting, since `{:q}` is `snakemake`-specific.
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For tracking performance and errors across backend and workers