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('HbTtvZFSPzHD0000'), started new Run('8d2GlAv9...') at 2025-06-03 11:33:15 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("HbTtvZFSPzHD", params={...})
! folder i[redun] Run Job 4a6f98e4: bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/→ finished Run('8d2GlAv9') after 5s at 2025-06-03 11:33:21 UTC
File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/results.tgz, hash=d55f2568)
Job b16c901c: bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/GKJHSjbhrGeYXC4w0000.fasta, hash=8203aa0f), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run Job f41e864c: bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/q8dS5YKudx54PfoG0000.fasta, hash=1d037baa), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run Job 705b9ab7: bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/CzfojJdi5A1xEqxI0000.fasta, hash=186de01c), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run Job 239c5179: bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/5RNv7y6BaPFE2m2E0000.fasta, hash=673ebe4e), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/5RNv7y6BaPFE2m2E0000.peptides.txt, hash=99227117), amino_acid='C') on default
[redun] Run Job e7c73f56: bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/GKJHSjbhrGeYXC4w0000.fasta, hash=8203aa0f), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/GKJHSjbhrGeYXC4w0000.peptides.txt, hash=f8cd0794), amino_acid='C') on default
[redun] Run Job ee26fec5: bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/q8dS5YKudx54PfoG0000.fasta, hash=1d037baa), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/q8dS5YKudx54PfoG0000.peptides.txt, hash=bed48b67), amino_acid='C') on default
[redun] Run Job ce93eef0: bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/CzfojJdi5A1xEqxI0000.fasta, hash=186de01c), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/CzfojJdi5A1xEqxI0000.peptides.txt, hash=db7d2268), amino_acid='C') on default
[redun] Run Job a69ca342: bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/5RNv7y6BaPFE2m2E0000.count.tsv, hash=c78d2161)) on default
[redun] Run Job d81c21b1: bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/GKJHSjbhrGeYXC4w0000.count.tsv, hash=95ad9021)) on default
[redun] Run Job d21d43bb: bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/q8dS5YKudx54PfoG0000.count.tsv, hash=1d3e627f)) on default
[redun] Run Job c4fef3df: bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/CzfojJdi5A1xEqxI0000.count.tsv, hash=b1dab632)) on default
[redun] Run Job 328ba69f: bioinformatics_pipeline_tutorial.lib.get_report_task(input_counts=[File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/5RNv7y6BaPFE2m2E0000.count.tsv, hash=c78d2161), File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-l...) on default
[redun] Run Job 3d7456cd: bioinformatics_pipeline_tutorial.lib.archive_results_task(inputs_plots=[File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/5RNv7y6BaPFE2m2E0000.plot.png, hash=7326aa0d), 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=71ade92d)) on default
[redun] Run Job 3ca254cb: redun_lamin_fasta.finish(results_archive=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/results.tgz, hash=d55f2568)) on default
[redun]
[redun] | JOB STATUS 2025/06/03 11:33:21
[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: 6.02 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='8d2GlAv9LUnA8ffW', started_at=2025-06-03 11:33:15 UTC, finished_at=2025-06-03 11:33:21 UTC, reference='563ec7b4-cf07-4b29-9e64-fbe19d378b34', 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=2025-06-03 11:33:15 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='8d2GlAv9LUnA8ffW', started_at=2025-06-03 11:33:15 UTC, finished_at=2025-06-03 11:33:21 UTC, reference='563ec7b4-cf07-4b29-9e64-fbe19d378b34', 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=2025-06-03 11:33:15 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 | V1SaYTVAmbtGAnbA0000 | None | Redun run report of 563ec7b4-cf07-4b29-9e64-fb... | .txt | None | None | 6335 | E9WAu-H5XadPHKMx15_a-g | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-06-03 11:33:25.588000+00:00 | 1 | None | 1 |
| 7 | mSISzUSz3FLnaHhT0000 | None | log streams of run 8d2GlAv9LUnA8ffW | .txt | __lamindb_run__ | None | 0 | 1B2M2Y8AsgTpgAmY7PhCfg | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-06-03 11:33:21.137000+00:00 | 1 | None | 1 |
| 6 | jQ4r76xgNbmviEqT0000 | None | requirements.txt | .txt | __lamindb_run__ | None | 3199 | vsG9AhFOE9HzvFSTWZ3-sA | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-06-03 11:33:21.131000+00:00 | 1 | None | 1 |
| 5 | r6HCsLemQJ9jtKlb0000 | data/results.tgz | None | .tgz | None | None | 83523 | 9qZX3m6HiDfUSdzFLWcnCg | None | None | md5 | False | False | 1 | 1 | None | None | True | 1.0 | 2025-06-03 11:33:21.071000+00:00 | 1 | None | 1 |
| 4 | CzfojJdi5A1xEqxI0000 | fasta/MYC.fasta | None | .fasta | None | None | 536 | WGbEtzPw-3bQEGcngO_pHQ | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-06-03 11:33:18.201000+00:00 | 1 | None | 1 |
| 2 | GKJHSjbhrGeYXC4w0000 | fasta/SOX2.fasta | None | .fasta | None | None | 414 | C5q_yaFXGk4SAEpfdqBwnQ | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-06-03 11:33:18.200000+00:00 | 1 | None | 1 |
| 3 | q8dS5YKudx54PfoG0000 | fasta/KLF4.fasta | None | .fasta | None | None | 609 | LyuoYkWs4SgYcH7P7JLJtA | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-06-03 11:33:18.200000+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 | pPMUPo11Otjp | input_dir | str | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-06-03 11:33:15.560000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
| 2 | 6x4PhdlbbRog | amino_acid | str | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-06-03 11:33:15.560000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
| 3 | 2qrtGhlL6S7K | enzyme_regex | str | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-06-03 11:33:15.560000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
| 4 | rDaFPTcb7Ky1 | missed_cleavages | int | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-06-03 11:33:15.560000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
| 5 | uBEd0Sjy5HTP | min_length | int | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-06-03 11:33:15.560000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
| 6 | AYuTwriiUYMd | max_length | int | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-06-03 11:33:15.560000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
| 7 | 4BjwAg9ueGZh | executor | str | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-06-03 11:33:15.560000+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 | 2025-06-03 11:33:15.596000+00:00 | 1 | None | 1 |
| 2 | C | DWH4NwytHUEvgLhNFD4SVw | 1 | 2 | None | 2025-06-03 11:33:15.598000+00:00 | 1 | None | 1 |
| 3 | [KR] | zPuapwAPylpfWRQFOTw9Cg | 1 | 3 | None | 2025-06-03 11:33:15.600000+00:00 | 1 | None | 1 |
| 4 | 0 | z80ghJXVZe9m59_5-Ydk2g | 1 | 4 | None | 2025-06-03 11:33:15.602000+00:00 | 1 | None | 1 |
| 5 | 4 | qH_2eaLz5x2RgaZ7dUISLA | 1 | 5 | None | 2025-06-03 11:33:15.604000+00:00 | 1 | None | 1 |
| 6 | 75 | 0Jv0FUSjNlpGyQd-u141ww | 1 | 6 | None | 2025-06-03 11:33:15.607000+00:00 | 1 | None | 1 |
| 7 | Executor.default | BaNJiQQLvaFrvOtdglHU7w | 1 | 7 | None | 2025-06-03 11:33:15.609000+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 | 8d2GlAv9LUnA8ffW | None | 2025-06-03 11:33:15.577513+00:00 | 2025-06-03 11:33:21.133532+00:00 | 563ec7b4-cf07-4b29-9e64-fbe19d378b34 | redun_id | True | 0 | 1 | 1 | 8 | None | 6 | None | 2025-06-03 11:33:15.578000+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 | Ceh2Hyk3e54n | /home/runner/work/redun-lamin/redun-lamin/docs... | None | local | None | iQlBPgD8uaqR | 1 | None | 2025-06-03 11:32:57.891000+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 | HbTtvZFSPzHD0000 | workflow.py | workflow.py | script | """workflow.py."""\n\n# This code is a copy fr... | mHyxrE622q2fluxICu4XDw | None | None | 1 | None | None | True | 2025-06-03 11:33:15.575000+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