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

Amend the workflow¶

import lamindb as ln
import json

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

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 Hide code cell output

→ connected lamindb: testuser1/test-redun-lamin
→ script invoked with: run workflow.py main --input-dir ./fasta --tag run=test-run
→ created Transform('GetkML6ddQwO0000', key='workflow.py'), started new Run('CHkRVeo4yLKvfLxB') at 2026-01-21 14:13:52 UTC
→ params: input_dir='./fasta', amino_acid='C', enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75, executor=<Executor.default: 'default'>
9[redun] Run    Job 86cdfb79:  bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/NDGn1AHnJVLoL6k10000.fasta, hash=f0194bee), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run    Job a1a6c3f9:  bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/hoFile(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/results.tgz, hash=36aa35be)
4d0c), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run    Job e2625ed7:  bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/anYEAKqv0fyYs3M30000.fasta, hash=4b4d0ac9), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run    Job 967fdd29:  bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/uZ0CCdMwjnsJt59G0000.fasta, hash=e3710452), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run    Job 500dc9a2:  bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/NDGn1AHnJVLoL6k10000.fasta, hash=f0194bee), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/NDGn1AHnJVLoL6k10000.peptides.txt, hash=333f7c69), amino_acid='C') on default
[redun] Run    Job f95ad4c0:  bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/IEoCeUF0UUnrfQnB0000.fasta, hash=fe284d0c), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/IEoCeUF0UUnrfQnB0000.peptides.txt, hash=b72f1c88), amino_acid='C') on default
[redun] Run    Job ea5b1b17:  bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/anYEAKqv0fyYs3M30000.fasta, hash=4b4d0ac9), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/anYEAKqv0fyYs3M30000.peptides.txt, hash=52fb23a4), amino_acid='C') on default
[redun] Run    Job 285e6b93:  bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/uZ0CCdMwjnsJt59G0000.fasta, hash=e3710452), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/uZ0CCdMwjnsJt59G0000.peptides.txt, hash=c6b27105), amino_acid='C') on default
[redun] Run    Job 81997d6b:  bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/NDGn1AHnJVLoL6k10000.count.tsv, hash=6447a1d4)) on default
[redun] Run    Job a364b839:  bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/IEoCeUF0UUnrfQnB0000.count.tsv, hash=f3decf3f)) on default
[redun] Run    Job d2f1367d:  bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/anYEAKqv0fyYs3M30000.count.tsv, hash=8219727a)) on default
[redun] Run    Job e1737513:  bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/uZ0CCdMwjnsJt59G0000.count.tsv, hash=4692bf8a)) on default
[redun] Run    Job 6085c050:  bioinformatics_pipeline_tutorial.lib.get_report_task(input_counts=[File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/NDGn1AHnJVLoL6k10000.count.tsv, hash=6447a1d4), File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-l...) on default
[redun] Run    Job 86d0be64:  bioinformatics_pipeline_tutorial.lib.archive_results_task(inputs_plots=[File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/NDGn1AHnJVLoL6k10000.plot.png, hash=aa546873), 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=6203469f)) on default
[redun] Run    Job e0860eee:  redun_lamin_fasta.finish(results_archive=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/results.tgz, hash=36aa35be)) on default
[redun] 
[redun] | JOB STATUS 2026/01/21 14:14:08
[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: 16.54 seconds

View data lineage:

artifact = ln.Artifact.get(key="data/results.tgz")
artifact.view_lineage()

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='CHkRVeo4yLKvfLxB', name=None, entrypoint=None, started_at=2026-01-21 14:13:52 UTC, finished_at=2026-01-21 14:14:08 UTC, params={'input_dir': './fasta', 'amino_acid': 'C', 'enzyme_regex': '[KR]', 'missed_cleavages': 0, 'min_length': 4, 'max_length': 75, 'executor': 'default'}, reference='8b7aae3c-a953-44b3-b29f-1abd5e758890', reference_type='redun_id', cli_args='run workflow.py main --input-dir ./fasta --tag run=test-run', branch_id=1, space_id=1, transform_id=1, report_id=7, environment_id=1, created_by_id=3, initiated_by_run_id=None, created_at=2026-01-21 14:13:52 UTC, is_locked=False)

Track the redun run report¶

While lamindb tracks logs of the main python process, the redun logs currently don’t get tracked and artifact.run.report is an empty text file.

This is how you can manually attach a report.

report = ln.Artifact(
    "run_logs.txt",
    description=f"Redun run report of {redun_exec['id']}",
    run=False,
    kind="__lamindb_run__",  # mark as auxiliary artifact for the run
).save()
artifact.run.report = report
artifact.run.save()

Run(uid='CHkRVeo4yLKvfLxB', name=None, entrypoint=None, started_at=2026-01-21 14:13:52 UTC, finished_at=2026-01-21 14:14:08 UTC, params={'input_dir': './fasta', 'amino_acid': 'C', 'enzyme_regex': '[KR]', 'missed_cleavages': 0, 'min_length': 4, 'max_length': 75, 'executor': 'default'}, reference='8b7aae3c-a953-44b3-b29f-1abd5e758890', reference_type='redun_id', cli_args='run workflow.py main --input-dir ./fasta --tag run=test-run', branch_id=1, space_id=1, transform_id=1, report_id=8, environment_id=1, created_by_id=3, initiated_by_run_id=None, created_at=2026-01-21 14:13:52 UTC, is_locked=False)

View transforms and runs in LaminHub¶

View the database content¶

ln.view()

Show code cell output Hide code cell output

Artifact

	uid	key	description	suffix	kind	otype	size	hash	n_files	n_observations	version_tag	is_latest	is_locked	created_at	branch_id	space_id	storage_id	run_id	schema_id	created_by_id
id
6	j8qS0k3HYGM32YjR0000	data/results.tgz	None	.tgz	None	None	94331	PLgZpTlex_hTxCOel4fBPQ	None	None	None	True	False	2026-01-21 14:14:08.654000+00:00	1	1	3	1.0	None	3
5	uZ0CCdMwjnsJt59G0000	fasta/KLF4.fasta	None	.fasta	None	None	609	LyuoYkWs4SgYcH7P7JLJtA	None	None	None	True	False	2026-01-21 14:13:53.121000+00:00	1	1	3	NaN	None	3
4	anYEAKqv0fyYs3M30000	fasta/PO5F1.fasta	None	.fasta	None	None	477	-7iJgveFO9ia0wE1bqVu6g	None	None	None	True	False	2026-01-21 14:13:53.120000+00:00	1	1	3	NaN	None	3
3	IEoCeUF0UUnrfQnB0000	fasta/MYC.fasta	None	.fasta	None	None	536	WGbEtzPw-3bQEGcngO_pHQ	None	None	None	True	False	2026-01-21 14:13:53.120000+00:00	1	1	3	NaN	None	3
2	NDGn1AHnJVLoL6k10000	fasta/SOX2.fasta	None	.fasta	None	None	414	C5q_yaFXGk4SAEpfdqBwnQ	None	None	None	True	False	2026-01-21 14:13:53.119000+00:00	1	1	3	NaN	None	3

Run

	uid	name	entrypoint	started_at	finished_at	params	reference	reference_type	cli_args	is_locked	created_at	branch_id	space_id	transform_id	report_id	environment_id	created_by_id	initiated_by_run_id
id
1	CHkRVeo4yLKvfLxB	None	None	2026-01-21 14:13:52.369438+00:00	2026-01-21 14:14:08.689929+00:00	{'input_dir': './fasta', 'amino_acid': 'C', 'e...	8b7aae3c-a953-44b3-b29f-1abd5e758890	redun_id	run workflow.py main --input-dir ./fasta --tag...	False	2026-01-21 14:13:52.370000+00:00	1	1	1	8	1	3	None

Storage

	uid	root	description	type	region	instance_uid	is_locked	created_at	branch_id	space_id	created_by_id	run_id
id
3	oEwaELVLOWvy	/home/runner/work/redun-lamin/redun-lamin/docs...	None	local	None	iQlBPgD8uaqR	False	2026-01-21 14:13:42.584000+00:00	1	1	3	None

Transform

	uid	key	description	kind	source_code	hash	reference	reference_type	version_tag	is_latest	is_locked	created_at	branch_id	space_id	environment_id	created_by_id
id
1	GetkML6ddQwO0000	workflow.py	None	script	"""workflow.py."""\n\n# This code is a copy fr...	Qn4m7TedTE04S_x3VFxq8w	None	None	None	True	False	2026-01-21 14:13:52.341000+00:00	1	1	None	3

Delete the test instance: