add phynest#621
Open
alxndrdiaz wants to merge 1 commit into
Open
Conversation
Collaborator
|
No test-cmds.txt (test file) present, skipping tests |
There was a problem hiding this comment.
Pull request overview
This PR adds a new BioContainers image definition for PhyNEST 0.1.12 by introducing a Dockerfile under the standard tool/version/ layout.
Changes:
- Added
phynest/0.1.12/Dockerfileusing thebiocontainers/biocontainers:v1.0.0_cv5base image. - Included BioContainers metadata labels (software, version, homepage, license, etc.).
- Installs Julia via
juliaupand adds thePhyNESTJulia package at version0.1.12.
Comment on lines
+19
to
+23
| RUN curl -fsSL https://install.julialang.org | sh -s -- -y | ||
|
|
||
| ENV PATH="/home/biodocker/.juliaup/bin:$PATH" | ||
|
|
||
| RUN julia -e 'using Pkg; Pkg.add(name="PhyNEST", version="0.1.12")' No newline at end of file |
Contributor
Author
There was a problem hiding this comment.
There is no environment variable "JULIA_CHANNEL", see latest documentation:
Environment Variables
pull Bot
pushed a commit
to bgruening/containers
that referenced
this pull request
Jul 7, 2026
…S3 fix Detection layers so a container PR never merges with unreviewed 'strange' content (e.g. BioContainers#621's `curl | sh`): - validate.py: scan_dockerfile_risks() lifts the lines a human must sign off on into the PR comment as an advisory reviewer checklist (curl|sh, http://, ADD <url>, paste/shortener/bare-IP hosts, chmod 777, --insecure, odd base image). High-confidence embedded credentials (AWS/GitHub/Slack tokens, private keys) block the PR. Line-continuations are folded so a split `curl \<nl>| sh` cannot evade; download rules are scoped to RUN/ADD/COPY so an http:// homepage in a LABEL is not a false positive. 12 new unit tests. - pr-report.yml: render the checklist + a bioconda-style 'build & test locally' block (and point at the existing test-cmds.txt convention). - Copilot: .github/copilot-instructions.md + instructions/dockerfile.instructions.md so automatic Copilot review hunts the same risks on every container PR. - publish.yml: fix Singularity S3 upload on Ceph/RGW (aws-cli v2.23+ default checksums broke multipart; set *_CHECKSUM to when_required).
Contributor
Author
|
Copilot mentions an environment variable "JULIA_CHANNEL" that apparently does not exists, see latest documentation: |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Submitting a Container
(If you're requesting for a new container, please check the procedure described here.
Check BioContainers' Dockerfile specifications
Checklist
Check BioContainers' Dockerfile metadata