Shell Commands

lint

TPV config files can be checked for linting errors using the tpv lint command.

tpv lint <url_or_path_to_config_file>

If linting is successful, a lint successful message will be displayed with an exit code of zero. If the linting fails, a lint failed message with the relevant error will be displayed with an exit code of 1. For example:

$ cat >good.yml <<EOF
tools:
  default:
    cores: 1
    mem: cores * 3.9
    context:
      partition: normal
    params:
      native_specification: "--nodes=1 --ntasks={cores} --ntasks-per-node={cores} --mem={round(mem*1024)} --partition={partition}"
    scheduling:
      reject:
        - offline
    rules: []
EOF
$ tpv lint good.yml
INFO : tpv.commands.shell: lint successful.
$ echo $?
0

cat >bad.yml <<EOF
tools:
  - default:
      cores: 1
EOF
$ tpv lint bad.yml
INFO : tpv.commands.shell: lint failed.
$ echo $?
1

To display the reasons for the failure, use the -v option to increase verbosity, with each additional v increasing log level.

dry-run

You can test that your TPV configuration returns the expected destination for a given tool and/or user using the tpv dry-run command.

tpv dry-run --job-conf <path_to_galaxy_job_conf_file> [--tool <tool_id>] \
    [--user <user_name_or_email>] [--input-size <size_in_gb>] \
    [tpv_config_file ...]

If no TPV config files are specified on the command line, they will be read from the tpv_dispatcher execution environment (destination) definition in the specified Galaxy job configuration file.

For example:

$ tpv dry-run --job-conf /srv/galaxy/config/job_conf.yml
!!python/object:galaxy.jobs.JobDestination
converted: false
env:
- {name: LC_ALL, value: C}
id: slurm
legacy: false
params: {native_specification: --nodes=1 --ntasks=1 --ntasks-per-node=1 --mem=3994
    --partition=normal, outputs_to_working_directory: true, tmp_dir: true}
resubmit: []
runner: slurm
shell: null
tags: null
url: null

$ tpv dry-run --job-conf /srv/galaxy/config/job_conf.yml --tool trinity --input-size 40 *.yml
!!python/object:galaxy.jobs.JobDestination
converted: false
env:
- {name: LC_ALL, value: C}
- {name: TERM, value: vt100}
- {execute: ulimit -c 0}
- {execute: ulimit -u 16384}
id: pulsar
legacy: false
params:
  default_file_action: remote_transfer
  dependency_resolution: remote
  jobs_directory: /scratch/pulsar/staging
  outputs_to_working_directory: false
  remote_metadata: false
  rewrite_parameters: true
  submit_native_specification: --nodes=1 --ntasks=20 --ntasks-per-node=20 --partition=xlarge
  transport: curl
resubmit: []
runner: pulsar
shell: null
tags: null
url: null