Redun¶
Here, we’ll see how to track redun workflow runs with LaminDB.
Note
This use case is based on github.com/ricomnl/bioinformatics-pipeline-tutorial.
# pip install lamindb redun git+http://github.com/laminlabs/redun-lamin-fasta
!lamin init --storage ./test-redun-lamin
Show code cell output
→ initialized lamindb: testuser1/test-redun-lamin
Amend the workflow¶
import lamindb as ln
import json
Show code cell output
→ connected lamindb: testuser1/test-redun-lamin
Let’s amend a redun workflow.py to register input & output artifacts in LaminDB:
To track the workflow run in LaminDB, add (see on GitHub):
ln.track(params=params)
To register the output file via LaminDB, add (see on GitHub):
ln.Artifact(output_path, description="results").save()
Run redun¶
Let’s see what the input files are:
!ls ./fasta
Show code cell output
KLF4.fasta MYC.fasta PO5F1.fasta SOX2.fasta
And call the workflow:
!redun run workflow.py main --input-dir ./fasta --tag run=test-run 1> run_logs.txt 2>run_logs.txt
Inspect the logs:
!cat run_logs.txt
Show code cell output
→ connected lamindb: testuser1/test-redun-lamin
→ created Transform('LTOdVguX9YMQ0000'), started new Run('lfEZxI77...') at 2025-05-29 10:20:46 UTC
→ params: input_dir=./fasta, amino_acid=C, enzyme_regex=[KR], missed_cleavages=0, min_length=4, max_length=75, executor=Executor.default
• recommendation: to identify the script across renames, pass the uid: ln.track("LTOdVguX9YMQ", params={...})
! folder i[redun] Run Job 58d67bba: bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/→ finished Run('lfEZxI77') after 5s at 2025-05-29 10:20:51 UTC
File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/results.tgz, hash=dac42831)
Job 37594679: bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/2pUI05ZkqRq1DqgT0000.fasta, hash=cb70c8b2), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run Job bd1908b5: bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/KjAO7D6HP2jBj5x90000.fasta, hash=bd819407), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run Job 211b2912: bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/iF5WgnltSL0TOjF20000.fasta, hash=a3bac78e), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run Job 56e360e7: bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/chd7f8CWrwoRckUl0000.fasta, hash=b6e846d3), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/chd7f8CWrwoRckUl0000.peptides.txt, hash=5e6cd48b), amino_acid='C') on default
[redun] Run Job 00e793d3: bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/2pUI05ZkqRq1DqgT0000.fasta, hash=cb70c8b2), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/2pUI05ZkqRq1DqgT0000.peptides.txt, hash=8d6e9b47), amino_acid='C') on default
[redun] Run Job bb10c82e: bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/KjAO7D6HP2jBj5x90000.fasta, hash=bd819407), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/KjAO7D6HP2jBj5x90000.peptides.txt, hash=4009aaca), amino_acid='C') on default
[redun] Run Job a95ebe83: bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/iF5WgnltSL0TOjF20000.fasta, hash=a3bac78e), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/iF5WgnltSL0TOjF20000.peptides.txt, hash=04b31547), amino_acid='C') on default
[redun] Run Job bb95444f: bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/chd7f8CWrwoRckUl0000.count.tsv, hash=1ff0ca15)) on default
[redun] Run Job 1c208177: bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/2pUI05ZkqRq1DqgT0000.count.tsv, hash=f901c9f2)) on default
[redun] Run Job aa3e47b4: bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/KjAO7D6HP2jBj5x90000.count.tsv, hash=b0ac78c6)) on default
[redun] Run Job 16654ed5: bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/iF5WgnltSL0TOjF20000.count.tsv, hash=f4f0dd46)) on default
[redun] Run Job 52ab5796: bioinformatics_pipeline_tutorial.lib.get_report_task(input_counts=[File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/chd7f8CWrwoRckUl0000.count.tsv, hash=1ff0ca15), File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-l...) on default
[redun] Run Job 849f284a: bioinformatics_pipeline_tutorial.lib.archive_results_task(inputs_plots=[File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/chd7f8CWrwoRckUl0000.plot.png, hash=7450a81e), File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-la..., input_report=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/protein_report.tsv, hash=528cd7aa)) on default
[redun] Run Job 7005f86e: redun_lamin_fasta.finish(results_archive=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/results.tgz, hash=dac42831)) on default
[redun]
[redun] | JOB STATUS 2025/05/29 10:20:51
[redun] | TASK PENDING RUNNING FAILED CACHED DONE TOTAL
[redun] |
[redun] | ALL 0 0 0 0 16 16
[redun] | bioinformatics_pipeline_tutorial.lib.archive_results_task 0 0 0 0 1 1
[redun] | bioinformatics_pipeline_tutorial.lib.count_amino_acids_task 0 0 0 0 4 4
[redun] | bioinformatics_pipeline_tutorial.lib.digest_protein_task 0 0 0 0 4 4
[redun] | bioinformatics_pipeline_tutorial.lib.get_report_task 0 0 0 0 1 1
[redun] | bioinformatics_pipeline_tutorial.lib.plot_count_task 0 0 0 0 4 4
[redun] | redun_lamin_fasta.finish 0 0 0 0 1 1
[redun] | redun_lamin_fasta.main 0 0 0 0 1 1
[redun]
[redun]
[redun] Execution duration: 5.83 seconds
View data lineage:
artifact = ln.Artifact.get(key="data/results.tgz")
artifact.view_lineage()
Show code cell output
Track the redun execution id¶
If we want to be able to query LaminDB for redun execution ID, this here is a way to get it:
# export the run information from redun
!redun log --exec --exec-tag run=test-run --format json --no-pager > redun_exec.json
# load the redun execution id from the JSON and store it in the LaminDB run record
with open("redun_exec.json") as file:
redun_exec = json.loads(file.readline())
artifact.run.reference = redun_exec["id"]
artifact.run.reference_type = "redun_id"
artifact.run.save()
Run(uid='lfEZxI77Rmno8EZX', started_at=2025-05-29 10:20:46 UTC, finished_at=2025-05-29 10:20:51 UTC, reference='0aca03f7-deab-499d-a26f-a537e1bb4bd4', reference_type='redun_id', branch_id=1, space_id=1, transform_id=1, report_id=7, environment_id=6, created_by_id=1, created_at=2025-05-29 10:20:46 UTC)
Track the redun run report¶
Attach a run report:
report = ln.Artifact(
"run_logs.txt",
description=f"Redun run report of {redun_exec['id']}",
run=False,
visibility=0,
).save()
artifact.run.report = report
artifact.run.save()
Run(uid='lfEZxI77Rmno8EZX', started_at=2025-05-29 10:20:46 UTC, finished_at=2025-05-29 10:20:51 UTC, reference='0aca03f7-deab-499d-a26f-a537e1bb4bd4', reference_type='redun_id', branch_id=1, space_id=1, transform_id=1, report_id=8, environment_id=6, created_by_id=1, created_at=2025-05-29 10:20:46 UTC)
View transforms and runs in LaminHub¶
View the database content¶
ln.view()
Show code cell output
Artifact
| uid | key | description | suffix | kind | otype | size | hash | n_files | n_observations | _hash_type | _key_is_virtual | _overwrite_versions | space_id | storage_id | schema_id | version | is_latest | run_id | created_at | created_by_id | _aux | branch_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||||||
| 8 | khii6AZ7tlBv0Vil0000 | None | Redun run report of 0aca03f7-deab-499d-a26f-a5... | .txt | None | None | 6335 | p4YxXoleHKuNXX5F3MMRrA | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-05-29 10:20:56.297000+00:00 | 1 | None | 1 |
| 7 | TxjDSGrv7Fw4eaxm0000 | None | log streams of run lfEZxI77Rmno8EZX | .txt | __lamindb_run__ | None | 0 | 1B2M2Y8AsgTpgAmY7PhCfg | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-05-29 10:20:51.444000+00:00 | 1 | None | 1 |
| 6 | 0daFaKAYq4flGOMq0000 | None | requirements.txt | .txt | __lamindb_run__ | None | 3199 | OHN8RpjDlpZL9ALKeXRzHg | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-05-29 10:20:51.437000+00:00 | 1 | None | 1 |
| 5 | gH9czXGbnoDGs8H70000 | data/results.tgz | None | .tgz | None | None | 83677 | EHLMLTyhLHG9XowXsMI2Aw | None | None | md5 | False | False | 1 | 1 | None | None | True | 1.0 | 2025-05-29 10:20:51.386000+00:00 | 1 | None | 1 |
| 4 | iF5WgnltSL0TOjF20000 | fasta/KLF4.fasta | None | .fasta | None | None | 609 | LyuoYkWs4SgYcH7P7JLJtA | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-05-29 10:20:48.937000+00:00 | 1 | None | 1 |
| 3 | KjAO7D6HP2jBj5x90000 | fasta/PO5F1.fasta | None | .fasta | None | None | 477 | -7iJgveFO9ia0wE1bqVu6g | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-05-29 10:20:48.936000+00:00 | 1 | None | 1 |
| 2 | 2pUI05ZkqRq1DqgT0000 | fasta/MYC.fasta | None | .fasta | None | None | 536 | WGbEtzPw-3bQEGcngO_pHQ | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-05-29 10:20:48.935000+00:00 | 1 | None | 1 |
Feature
| uid | name | dtype | is_type | unit | description | array_rank | array_size | array_shape | proxy_dtype | synonyms | _expect_many | _curation | space_id | type_id | run_id | created_at | created_by_id | _aux | branch_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||||||
| 1 | 79fWYtpll9aT | input_dir | str | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-05-29 10:20:46.083000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
| 2 | dXxu65Yt8Wdw | amino_acid | str | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-05-29 10:20:46.083000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
| 3 | AlxXtZDr3ACn | enzyme_regex | str | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-05-29 10:20:46.083000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
| 4 | LrO5GTFKnpHp | missed_cleavages | int | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-05-29 10:20:46.083000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
| 5 | qnADaoEMVOl1 | min_length | int | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-05-29 10:20:46.083000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
| 6 | y98bPrkiZsxE | max_length | int | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-05-29 10:20:46.083000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
| 7 | AWJDEIr3trvH | executor | str | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-05-29 10:20:46.083000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
FeatureValue
| value | hash | space_id | feature_id | run_id | created_at | created_by_id | _aux | branch_id | |
|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||
| 1 | ./fasta | G8diGhDfCu78R1WbXfsHOw | 1 | 1 | None | 2025-05-29 10:20:46.119000+00:00 | 1 | None | 1 |
| 2 | C | DWH4NwytHUEvgLhNFD4SVw | 1 | 2 | None | 2025-05-29 10:20:46.121000+00:00 | 1 | None | 1 |
| 3 | [KR] | zPuapwAPylpfWRQFOTw9Cg | 1 | 3 | None | 2025-05-29 10:20:46.125000+00:00 | 1 | None | 1 |
| 4 | 0 | z80ghJXVZe9m59_5-Ydk2g | 1 | 4 | None | 2025-05-29 10:20:46.127000+00:00 | 1 | None | 1 |
| 5 | 4 | qH_2eaLz5x2RgaZ7dUISLA | 1 | 5 | None | 2025-05-29 10:20:46.128000+00:00 | 1 | None | 1 |
| 6 | 75 | 0Jv0FUSjNlpGyQd-u141ww | 1 | 6 | None | 2025-05-29 10:20:46.130000+00:00 | 1 | None | 1 |
| 7 | Executor.default | BaNJiQQLvaFrvOtdglHU7w | 1 | 7 | None | 2025-05-29 10:20:46.132000+00:00 | 1 | None | 1 |
Run
| uid | name | started_at | finished_at | reference | reference_type | _is_consecutive | _status_code | space_id | transform_id | report_id | _logfile_id | environment_id | initiated_by_run_id | created_at | created_by_id | _aux | branch_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||||
| 1 | lfEZxI77Rmno8EZX | None | 2025-05-29 10:20:46.100326+00:00 | 2025-05-29 10:20:51.440244+00:00 | 0aca03f7-deab-499d-a26f-a537e1bb4bd4 | redun_id | True | 0 | 1 | 1 | 8 | None | 6 | None | 2025-05-29 10:20:46.101000+00:00 | 1 | None | 1 |
Storage
| uid | root | description | type | region | instance_uid | space_id | run_id | created_at | created_by_id | _aux | branch_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||
| 1 | J39ww19HlRZY | /home/runner/work/redun-lamin/redun-lamin/docs... | None | local | None | iQlBPgD8uaqR | 1 | None | 2025-05-29 10:20:24.256000+00:00 | 1 | None | 1 |
Transform
| uid | key | description | type | source_code | hash | reference | reference_type | space_id | _template_id | version | is_latest | created_at | created_by_id | _aux | branch_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||
| 1 | LTOdVguX9YMQ0000 | workflow.py | workflow.py | script | """workflow.py."""\n\n# This code is a copy fr... | mHyxrE622q2fluxICu4XDw | None | None | 1 | None | None | True | 2025-05-29 10:20:46.098000+00:00 | 1 | None | 1 |
Delete the test instance:
Show code cell content
!rm -rf test-redun-lamin
!lamin delete --force test-redun-lamin
• deleting instance testuser1/test-redun-lamin