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('73Wt9j2dxj1H0000'), started new Run('JgTS0g0x...') at 2025-04-15 16:33:24 UTC
→ params: input_dir=./fasta, amino_acid=C, enzyme_regex=[KR], missed_cleavages=0, min_length=4, max_length=75, executor=Executor.default
! folder is outside existing storage location, will copy files from ./fasta to /home/runner/work/redun-lamin/redun-lamin/docs/test-[redun] Run Job→ finished Run('JgTS0g0x') after 4s at 2025-04-15 16:33:28 UTC
File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/results.tgz, hash=352c96ea)
000.fasta, hash=699b7006), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run Job 1fde0a36: bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/4OcSccGHlzNrNkOs0000.fasta, hash=95b849e0), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run Job 01f01797: bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/CbSa0ol62HD6vxW70000.fasta, hash=acc3b019), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run Job 0825f16c: bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/r81MZjUjMV8r4ito0000.fasta, hash=c4cb1963), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run Job a0bfc460: bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/w5pWBrVFspTPQ0rE0000.fasta, hash=699b7006), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/w5pWBrVFspTPQ0rE0000.peptides.txt, hash=b3fc99ff), amino_acid='C') on default
[redun] Run Job a7361857: bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/4OcSccGHlzNrNkOs0000.fasta, hash=95b849e0), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/4OcSccGHlzNrNkOs0000.peptides.txt, hash=f4b029ad), amino_acid='C') on default
[redun] Run Job cb1510ab: bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/CbSa0ol62HD6vxW70000.fasta, hash=acc3b019), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/CbSa0ol62HD6vxW70000.peptides.txt, hash=7d01428b), amino_acid='C') on default
[redun] Run Job 4088c31f: bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/r81MZjUjMV8r4ito0000.fasta, hash=c4cb1963), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/r81MZjUjMV8r4ito0000.peptides.txt, hash=581b5516), amino_acid='C') on default
[redun] Run Job 9c3fa074: bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/w5pWBrVFspTPQ0rE0000.count.tsv, hash=19799282)) on default
[redun] Run Job f0d63475: bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/4OcSccGHlzNrNkOs0000.count.tsv, hash=a0b6d945)) on default
[redun] Run Job aebbf865: bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/CbSa0ol62HD6vxW70000.count.tsv, hash=02f7d3dd)) on default
[redun] Run Job f350da58: bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/r81MZjUjMV8r4ito0000.count.tsv, hash=fd974743)) on default
[redun] Run Job 922d1071: bioinformatics_pipeline_tutorial.lib.get_report_task(input_counts=[File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/w5pWBrVFspTPQ0rE0000.count.tsv, hash=19799282), File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-l...) on default
[redun] Run Job 9776eba7: bioinformatics_pipeline_tutorial.lib.archive_results_task(inputs_plots=[File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/w5pWBrVFspTPQ0rE0000.plot.png, hash=5459e184), 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=f9de8f1f)) on default
[redun] Run Job 1cde791a: redun_lamin_fasta.finish(results_archive=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/results.tgz, hash=352c96ea)) on default
[redun]
[redun] | JOB STATUS 2025/04/15 16:33:29
[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: 5.64 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='JgTS0g0x1MpChdqcuW8X', started_at=2025-04-15 16:33:24 UTC, finished_at=2025-04-15 16:33:28 UTC, reference='913e800e-49dc-4f83-83ac-14b03bec5254', reference_type='redun_id', space_id=1, transform_id=1, report_id=7, environment_id=6, created_by_id=1, created_at=2025-04-15 16:33:24 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='JgTS0g0x1MpChdqcuW8X', started_at=2025-04-15 16:33:24 UTC, finished_at=2025-04-15 16:33:28 UTC, reference='913e800e-49dc-4f83-83ac-14b03bec5254', reference_type='redun_id', space_id=1, transform_id=1, report_id=8, environment_id=6, created_by_id=1, created_at=2025-04-15 16:33:24 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_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||||||
| 5 | LUoqBphMkMUrIZIC0000 | data/results.tgz | None | .tgz | None | None | 83702 | EtTQJPB8es0-uA1tfEosPA | None | None | md5 | False | False | 1 | 1 | None | None | True | 1.0 | 2025-04-15 16:33:28.262000+00:00 | 1 | None | 1 |
| 4 | r81MZjUjMV8r4ito0000 | fasta/KLF4.fasta | None | .fasta | None | None | 609 | LyuoYkWs4SgYcH7P7JLJtA | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-04-15 16:33:25.477000+00:00 | 1 | None | 1 |
| 3 | CbSa0ol62HD6vxW70000 | fasta/MYC.fasta | None | .fasta | None | None | 536 | WGbEtzPw-3bQEGcngO_pHQ | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-04-15 16:33:25.476000+00:00 | 1 | None | 1 |
| 2 | 4OcSccGHlzNrNkOs0000 | fasta/SOX2.fasta | None | .fasta | None | None | 414 | C5q_yaFXGk4SAEpfdqBwnQ | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-04-15 16:33:25.475000+00:00 | 1 | None | 1 |
| 1 | w5pWBrVFspTPQ0rE0000 | fasta/PO5F1.fasta | None | .fasta | None | None | 477 | -7iJgveFO9ia0wE1bqVu6g | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-04-15 16:33:25.474000+00:00 | 1 | None | 1 |
Param
| name | dtype | is_type | _expect_many | space_id | type_id | run_id | created_at | created_by_id | _aux | _branch_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||
| 1 | input_dir | str | None | False | 1 | None | None | 2025-04-15 16:33:24.119000+00:00 | 1 | None | 1 |
| 2 | amino_acid | str | None | False | 1 | None | None | 2025-04-15 16:33:24.119000+00:00 | 1 | None | 1 |
| 3 | enzyme_regex | str | None | False | 1 | None | None | 2025-04-15 16:33:24.119000+00:00 | 1 | None | 1 |
| 4 | missed_cleavages | int | None | False | 1 | None | None | 2025-04-15 16:33:24.119000+00:00 | 1 | None | 1 |
| 5 | min_length | int | None | False | 1 | None | None | 2025-04-15 16:33:24.119000+00:00 | 1 | None | 1 |
| 6 | max_length | int | None | False | 1 | None | None | 2025-04-15 16:33:24.119000+00:00 | 1 | None | 1 |
| 7 | executor | str | None | False | 1 | None | None | 2025-04-15 16:33:24.119000+00:00 | 1 | None | 1 |
ParamValue
| value | hash | space_id | param_id | created_at | created_by_id | _aux | _branch_code | |
|---|---|---|---|---|---|---|---|---|
| id | ||||||||
| 1 | ./fasta | None | 1 | 1 | 2025-04-15 16:33:24.151000+00:00 | 1 | None | 1 |
| 2 | C | None | 1 | 2 | 2025-04-15 16:33:24.151000+00:00 | 1 | None | 1 |
| 3 | [KR] | None | 1 | 3 | 2025-04-15 16:33:24.151000+00:00 | 1 | None | 1 |
| 4 | 0 | None | 1 | 4 | 2025-04-15 16:33:24.151000+00:00 | 1 | None | 1 |
| 5 | 4 | None | 1 | 5 | 2025-04-15 16:33:24.151000+00:00 | 1 | None | 1 |
| 6 | 75 | None | 1 | 6 | 2025-04-15 16:33:24.151000+00:00 | 1 | None | 1 |
| 7 | Executor.default | None | 1 | 7 | 2025-04-15 16:33:24.151000+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_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||||
| 1 | JgTS0g0x1MpChdqcuW8X | None | 2025-04-15 16:33:24.131276+00:00 | 2025-04-15 16:33:28.320463+00:00 | 913e800e-49dc-4f83-83ac-14b03bec5254 | redun_id | True | 0 | 1 | 1 | 8 | None | 6 | None | 2025-04-15 16:33:24.132000+00:00 | 1 | None | 1 |
Storage
| uid | root | description | type | region | instance_uid | space_id | run_id | created_at | created_by_id | _aux | _branch_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||
| 1 | cW9hJxrGsmcm | /home/runner/work/redun-lamin/redun-lamin/docs... | None | local | None | iQlBPgD8uaqR | 1 | None | 2025-04-15 16:33:06.067000+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_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||
| 1 | 73Wt9j2dxj1H0000 | workflow.py | workflow.py | script | """workflow.py."""\n\n# This code is a copy fr... | mHyxrE622q2fluxICu4XDw | None | None | 1 | None | None | True | 2025-04-15 16:33:24.129000+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