"command": executable file not found in $PATH

[IvanWoo22]

Description:

When I used nextflow on our LSF sys, I always get an error Command 'ps' required by nextflow to collect task metrics cannot be found. After checking the .command.run file and my singularity, I found it is not a ps PATH problem but a command PATH problem.
The following is my own testing process.

singularity exec --pid -B \
  nfmethylseq nfmethylseq/methylseq/workflow/../singularity-images/depot.galaxyproject.org-singularity-bismark-0.24.0--hdfd78af_0.img \
  command -v ps &>/dev/null || { >&2 echo "Command 'ps' required by nextflow to collect task metrics cannot be found"; }
  # Command 'ps' required by nextflow to collect task metrics cannot be found

singularity exec --pid -B \
  nfmethylseq nfmethylseq/methylseq/workflow/../singularity-images/depot.galaxyproject.org-singularity-bismark-0.24.0--hdfd78af_0.img \
  command -v ps
  # FATAL:   "command": executable file not found in $PATH

singularity exec --pid -B \
  nfmethylseq nfmethylseq/methylseq/workflow/../singularity-images/depot.galaxyproject.org-singularity-bismark-0.24.0--hdfd78af_0.img \
  ps
  # PID   USER     TIME  COMMAND
  #  1 wangq     0:00 sinit
  # 15 wangq     0:00 /bin/ps

When I comment the line command -v ps &>/dev/null || { >&2 echo "Command 'ps' required by nextflow to collect task metrics cannot be found"; exit 1; } with # and run with bash .command.run, it worked without error.

So, how could I fix this problem or no longer have this line of code every time the .command.run files generated?

[mribeirodantas]

Hey, Ivan. There is a list of tools in the official documentation that must be installed where tasks are run. ps is one of them. A solution to your problem is to have ps installed in your container 😄