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('HDCKzJQP9LuA0000', key='workflow.py'), started new Run('tgcky4ItkOf0cOVo') at 2026-01-11 16:51:31 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 0f0bcce8:  bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/79Ugg9GxpUYrE8860000.fasta, hash=7c939094), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run    Job 3e6572d8:  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=b19f0a1e)
7e65), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run    Job b45caf66:  bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/ovz1avKZByJAngSL0000.fasta, hash=43b6b143), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run    Job 9524261e:  bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/2lHMfHgGJXk1GYZ70000.fasta, hash=3d53d2a7), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run    Job 81e77216:  bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/79Ugg9GxpUYrE8860000.fasta, hash=7c939094), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/79Ugg9GxpUYrE8860000.peptides.txt, hash=a30eb33f), amino_acid='C') on default
[redun] Run    Job 68db39d6:  bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/l5d8r09xqYuzeL3F0000.fasta, hash=da1a7e65), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/l5d8r09xqYuzeL3F0000.peptides.txt, hash=e9a7f1a3), amino_acid='C') on default
[redun] Run    Job c04161d7:  bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/ovz1avKZByJAngSL0000.fasta, hash=43b6b143), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/ovz1avKZByJAngSL0000.peptides.txt, hash=841b1417), amino_acid='C') on default
[redun] Run    Job c2617430:  bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/2lHMfHgGJXk1GYZ70000.fasta, hash=3d53d2a7), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/2lHMfHgGJXk1GYZ70000.peptides.txt, hash=d469bfb7), amino_acid='C') on default
[redun] Run    Job 667f1e8e:  bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/79Ugg9GxpUYrE8860000.count.tsv, hash=2b367ea1)) on default
[redun] Run    Job 5163caf3:  bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/l5d8r09xqYuzeL3F0000.count.tsv, hash=80aca311)) on default
[redun] Run    Job fa81c3fb:  bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/ovz1avKZByJAngSL0000.count.tsv, hash=d0924b4f)) on default
[redun] Run    Job de484b6f:  bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/2lHMfHgGJXk1GYZ70000.count.tsv, hash=7f938b1d)) on default
[redun] Run    Job c5330d8c:  bioinformatics_pipeline_tutorial.lib.get_report_task(input_counts=[File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/79Ugg9GxpUYrE8860000.count.tsv, hash=2b367ea1), File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-l...) on default
[redun] Run    Job c1ce87ee:  bioinformatics_pipeline_tutorial.lib.archive_results_task(inputs_plots=[File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/79Ugg9GxpUYrE8860000.plot.png, hash=bb08f0b3), 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=5e8b6352)) on default
[redun] Run    Job 9d14755e:  redun_lamin_fasta.finish(results_archive=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/results.tgz, hash=b19f0a1e)) on default
[redun] 
[redun] | JOB STATUS 2026/01/11 16:51:44
[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: 13.32 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='tgcky4ItkOf0cOVo', name=None, entrypoint=None, started_at=2026-01-11 16:51:31 UTC, finished_at=2026-01-11 16:51:44 UTC, params={'input_dir': './fasta', 'amino_acid': 'C', 'enzyme_regex': '[KR]', 'missed_cleavages': 0, 'min_length': 4, 'max_length': 75, 'executor': 'default'}, reference='5b343c5a-e961-4bb2-8476-a269a9cf2d02', 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=2026-01-11 16:51:31 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='tgcky4ItkOf0cOVo', name=None, entrypoint=None, started_at=2026-01-11 16:51:31 UTC, finished_at=2026-01-11 16:51:44 UTC, params={'input_dir': './fasta', 'amino_acid': 'C', 'enzyme_regex': '[KR]', 'missed_cleavages': 0, 'min_length': 4, 'max_length': 75, 'executor': 'default'}, reference='5b343c5a-e961-4bb2-8476-a269a9cf2d02', 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=2026-01-11 16:51:31 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	1IFIq9CAF10O5XUh0000	data/results.tgz	None	.tgz	None	None	94347	3Us3-nYvTDU5WzjnteVQ9A	None	None	None	True	False	2026-01-11 16:51:44.050000+00:00	1	1	3	1.0	None	3
5	2lHMfHgGJXk1GYZ70000	fasta/KLF4.fasta	None	.fasta	None	None	609	LyuoYkWs4SgYcH7P7JLJtA	None	None	None	True	False	2026-01-11 16:51:31.713000+00:00	1	1	3	NaN	None	3
4	ovz1avKZByJAngSL0000	fasta/PO5F1.fasta	None	.fasta	None	None	477	-7iJgveFO9ia0wE1bqVu6g	None	None	None	True	False	2026-01-11 16:51:31.713000+00:00	1	1	3	NaN	None	3
3	l5d8r09xqYuzeL3F0000	fasta/MYC.fasta	None	.fasta	None	None	536	WGbEtzPw-3bQEGcngO_pHQ	None	None	None	True	False	2026-01-11 16:51:31.712000+00:00	1	1	3	NaN	None	3
2	79Ugg9GxpUYrE8860000	fasta/SOX2.fasta	None	.fasta	None	None	414	C5q_yaFXGk4SAEpfdqBwnQ	None	None	None	True	False	2026-01-11 16:51:31.711000+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	tgcky4ItkOf0cOVo	None	None	2026-01-11 16:51:31.012370+00:00	2026-01-11 16:51:44.095530+00:00	{'input_dir': './fasta', 'amino_acid': 'C', 'e...	5b343c5a-e961-4bb2-8476-a269a9cf2d02	redun_id	run workflow.py main --input-dir ./fasta --tag...	False	2026-01-11 16:51:31.013000+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	B1Y6nnV9avxU	/home/runner/work/redun-lamin/redun-lamin/docs...	None	local	None	iQlBPgD8uaqR	False	2026-01-11 16:51:17.805000+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	HDCKzJQP9LuA0000	workflow.py	None	script	"""workflow.py."""\n\n# This code is a copy fr...	Qn4m7TedTE04S_x3VFxq8w	None	None	None	True	False	2026-01-11 16:51:31.010000+00:00	1	1	None	3

Delete the test instance: