Claude Code, Skill
Bio Gene To Reference Tree
Build the reference set before you build the tree.
Compatibility: Not stated.
Grade C
One Medium finding. Read the report before installing.
Not a guarantee. A hygiene check of the source at the commit shown, not a security audit.
PERMISSION_SHELL_UNDECLARED
Why this grade
- PERMISSION_SHELL_UNDECLARED Medium
Runs shell commands that the manifest or description does not mention.
examples/brca1/scripts/verify_brca1_qc_promotion.py, line 84
completed = subprocess.run(
Any High, or two or more Medium findings, give D. One Medium gives C. Low findings or a security Note give B. Each code names a finding behind the letter.
Grades are a hygiene check of the source at the commit shown, on the date checked, not a security audit or a guarantee. The free directory grades are automated. Before release, a PlugVet engineer reviews every paid report and any grade we hold back, including all F grades, against the source code and the evidence we quote.
What was checked
Plain notes from the hygiene checks.
Permissions
Concern
requests shell access. No manifest field names shell or command execution.
PERMISSION_SHELL_UNDECLARED
examples/brca1/scripts/verify_brca1_qc_promotion.py, line 84
completed = subprocess.run(
skills/bio-gene-to-reference-tree/scripts/gene_to_tree.py, line 3891
completed = subprocess.run(
skills/bio-gene-to-reference-tree/scripts/gene_to_tree.py, line 3969
completed = subprocess.run(
Install and update
Pass
No install-time script found, and dependencies are pinned or absent.
Network
Pass
No network call found.
Secrets
Concern
reads a credential or environment file.
SECRETS_PATH_UNCONFIRMED
.gitignore, line 7
.venv/
Agent instructions
Pass
No instruction to ignore earlier instructions or to hide a step.
Obfuscation
Note
a file was over the read cap and was not fully read.
OBFUSCATION_FILE_OVER_READ_CAP
examples/brca1/tree/iqtree/brca1-balanced.ufboot, line 1
(NP_009225.1:0.0135100000,((((XP_003414318.3:0.1557410000,XP_058140293.1:0.1151230000):0.0081210700,((((((XP_072775070.1:0.3534050000,NP_989500.1:0.3682720000):0.3160090000,XP_0194
skills/bio-gene-to-reference-tree/scripts/gene_to_tree.py, line 1
#!/usr/bin/env python3
Licence
Pass
A licence file is present (LICENSE).
Maintainer activity
Pass
The latest commit is within the last 365 days.
Note
Hygiene check of commit 94b23d9752e5. requests shell access. No manifest field names shell or command execution. reads a credential or environment file. a file was over the read cap and was not fully read.
Date and source
Date checked:
github.com
Commit graded: 94b23d9752e5b3a70f0dadea6505adcd04864ff1
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