(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 (try bsub -Is -R select[hname!='hl-codon-32-02'] bash for eg)
Pfew- long story short, I have found a simple solution to this, and putting in a PR with unit tests.
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.