Complex shell quote escaping fails #39
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bricoletc
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Mar 7, 2021
* The split argument string needs to be rejoined using `shlex` * Two unit tests for `lsf_config.py` to ensure quotes are shell-escaped * One modified unit test for `lsf_submit.py` to ensure quotes are shell-escaped * Rewrote `__init__` of `Config` object, to directly concatenate parameter lists. Makes downstream argument string production simpler to read. * Added function docstrings in `lsf_config.py` to make understanding easier
bricoletc
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Mar 7, 2021
* Add vim and ven to gitignore * Add Snakemake-Profiles#39 solving to changelog * Add example of complex quote escaping in readme
bricoletc
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Mar 7, 2021
* Add vim and ven to gitignore * Add Snakemake-Profiles#39 solving to changelog * Add example of complex quote escaping in readme
mbhall88
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Mar 12, 2021
* The split argument string needs to be rejoined using `shlex` * Two unit tests for `lsf_config.py` to ensure quotes are shell-escaped * One modified unit test for `lsf_submit.py` to ensure quotes are shell-escaped * Rewrote `__init__` of `Config` object, to directly concatenate parameter lists. Makes downstream argument string production simpler to read. * Added function docstrings in `lsf_config.py` to make understanding easier
mbhall88
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Mar 12, 2021
* Add vim and ven to gitignore * Add #39 solving to changelog * Add example of complex quote escaping in readme
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Hello,
I was trying to instruct snakemake to ignore a specific lsf host which is faulty, so wrote this in my
lsf.yaml:(This gets parsed as
{'__default__': ['-R "select[hname!=\'hl-codon-32-02\']"']}by pyyaml)The reason I do this is that if the hostname to ignore has special characters, the shell command needs to look like
-R "select[hname!='hname']"(see IBM docs :If you need to include a hyphen (-) or other non-alphabetic characters within the string, enclose the text in single quotation marks, for example, bsub -R "select[hname!='host06-x12']")However this gets passed at submission time as
-R select[hname!='hl-codon-32-02']but lsf cannot submit that (trybsub -Is -R select[hname!='hl-codon-32-02'] bashfor eg)Pfew- long story short, I have found a simple solution to this, and putting in a PR with unit tests.
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