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klebgenomics / Kleborate

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kaptive.py :: popen uses potentialy wrong python3 #49

Closed EricDeveaud closed 4 years ago

EricDeveaud commented 4 years ago

Hello,

in our setup we have python tools installed with specific python(2|3) that are not in the user path

so we have this error

bigmess:Kleborate/2.0.0 > kleborate -k -o details.txt -a ../../datas/Kleborate/Vibrio_cholerae_O1_biovar_eltor_str_N16961_v2.fasta
strain  species ST  virulence_score Yersiniabactin  YbST    Colibactin  CbST    Aerobactin  AbST    Salmochelin SmST    RmpADC  RmST    rmpA2   wzi K_locus K_locus_confidence  O_locus O_locus_confidence
Error: Kaptive failed to run with the following error:
/bin/sh: python3: command not found

it is good practive to use the exatct same interpreter the script is running to perform subcalls fix is quite easy: https://github.com/katholt/Kleborate/pull/48

regards

Eric

rrwick commented 4 years ago

Hi Eric,

Thanks for the PR - I've merged it in, so hopefully this will resolve the problem! I'll optimistically close this issue now, but please let me know if the problem persists.

Ryan