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Hi @anjos et. al,
I'm using gridtk with UGE and it seems to work. The only problem I've had is when using qsub -sync it circumvents the -terse functionality (see below). I was also unable to make any comments or issues in the GitLab instance where this repo is mirrored, so sorry if I missed something (?).
from gridtk.tools import qsub
qsub([jobscript],
sge_extra_args='-sync y -V')The following has output like this:
123456
Job 123456 exited with exit code 0.I tested the output in my python console with the code from the original traceback which pointed me here:
https://github.com/bioidiap/gridtk/blob/82d328d5f9de18ac569a6856175ed071d20ba998/src/gridtk/tools.py#L258C12-L258C55
# my test
>>> jobid = '123456\nJob 123456 exited with exit code 0.'
>>> int(jobid.split("\n")[-1].split(".", 1)[0])
Traceback (most recent call last):
File "/Users/gilmorera/Library/Caches/pypoetry/virtualenvs/gris-seqr-vcf-processing-3KNk8Ldu-py3.10/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 3548, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-31-408eaadb10e5>", line 1, in <module>
int(jobid.split("\n")[-1].split(".", 1)[0])
ValueError: invalid literal for int() with base 10: 'Job 123456 exited with exit code 0'Metadata
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