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thasso / pyjip

JIP Pipeline System
http://pyjip.readthedocs.org
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Check called binaries and scream if not found #47

Closed Poshi closed 10 years ago

Poshi commented 10 years ago

In short, when commands like sbatch are not in the path, the error message is cryptic.

$ sbatch -bash: sbatch: command not found $ jip submit gemtools_qcmapping_pipeline --load basic.json Error while submitting job: [Errno 2] No such file or directory

$ export PATH=/opt/perf/bin:$PATH $ which sbatch /opt/perf/bin/sbatch $ jip submit gemtools_qcmapping_pipeline --load basic.json Submitted 96 with remote id 13954408 . . .

Poshi commented 10 years ago

This issue has just been addressed with the recent merge in commit e95f4df4e115bcdbb4e57300b7d516eccbf639aa