cdm_psortb

CTS (CDM Task Service) job wrapper for PSORTb, bacterial protein subcellular localization prediction.

Container

Wraps the canonical brinkmanlab/psortb_commandline:1.0.2 image (released by the Brinkman lab, the developers of PSORTb).

Published to ghcr.io/kbaseincubator/cdm_psortb.

Entrypoint: /usr/local/psortb/bin/psort (the PSORTb CLI binary). Append PSORTb flags as arguments.

Reference data: Not required. PSORTb's models and SCL databases are bundled inside the container.

Usage via CTS

Required organism flag (one of):

• --positive for Gram-positive bacteria
• --negative for Gram-negative bacteria
• --archaea for archaea

Example

job = tscli.submit_job(
    "ghcr.io/kbaseincubator/cdm_psortb:0.1.0@sha256:<digest>",
    input_files,                         # protein FASTA files
    "cts/io/{your_username}/output/psortb/test/v1",
    cluster="kbase",
    declobber=True,
    output_mount_point="/out",
    args=[
        "--negative",                    # or --positive / --archaea
        "--output", "terse",             # terse | normal | long
        "--seqformat", "FASTA",
        "-o", "/out/psortb_results.txt",
        tscli.insert_files(),
    ],
    num_containers=4,
    cpus=4,
    memory="16GB",
    runtime="PT2H"
)

Output

PSORTb produces a single results file with predicted subcellular localization per protein. With --output terse (recommended for downstream parsing): three tab-separated columns: SeqID, Localization, Score.