Add LisSero 0.4.10 container#1724
Open
arodzh-sudo wants to merge 4 commits into
Open
Conversation
…ogroup typing Two-stage micromamba/bioconda Dockerfile (lissero 0.4.10, blast pulled by conda) with a test stage that serogroups the serotype 4b reference F2365 (GCF_000008285.1) and asserts the 4b, 4d, 4e call. Adds the image-table row to the root README and a GPLv3 entry to Program_Licenses.md.
Collaborator
|
Hi @arodzh-sudo |
Contributor
Author
|
Thanks @Kincekara. Switched the base image to mambaorg/micromamba:2.8.1-ubuntu24.04 in 91b6b27 |
erinyoung
reviewed
Jun 26, 2026
|
|
||
| Additional tools: | ||
| - ncbi-blast+ (blastn): >=2.10.0 | ||
|
|
Contributor
There was a problem hiding this comment.
Can you add a section in the readme that lists all of the packages installed via micromamba?
Specifically, I'm looking for the output of micromamba list -n base.
This is an example from the piranha image. It helps in troubleshooting issues.
<details>
<summary>Additional tools installed via micromamba:</summary>
List of packages in environment: "/opt/conda/envs/piranha"
Name Version Build Channel
──────────────────────────────────────────────────────────────────────────────────────────────────
Mako 1.2.0 pypi_0 pypi
_openmp_mutex 5.1 52_gnu pkgs/main
alsa-lib 1.2.16.1 hb03c661_0 conda-forge
appdirs 1.4.4 pyhd8ed1ab_1 conda-forge
argparse-dataclass 2.0.0 pyhd8ed1ab_1 conda-forge
attrs 26.1.0 pyhcf101f3_0 conda-forge
aws-c-auth 0.10.1 ha62d5e7_3 conda-forge
aws-c-cal 0.9.13 h2c9d079_1 conda-forge
aws-c-common 0.12.6 hb03c661_0 conda-forge
aws-c-compression 0.3.2 h8b1a151_0 conda-forge
aws-c-http 0.10.13 h4bacb7b_0 conda-forge
aws-c-io 0.26.3 hb18f61d_2 conda-forge
aws-c-s3 0.12.0 h1b28b03_1 pkgs/main
aws-c-sdkutils 0.2.4 h8b1a151_4 conda-forge
aws-checksums 0.2.10 h8b1a151_0 conda-forge
backports.zstd 1.6.0 py312h90b7ffd_0 conda-forge
tabix 1.11 hdfd78af_0 bioconda
tabixpp 1.1.2 hbefcdb2_4 bioconda
tabulate 0.10.0 pyhcf101f3_0 conda-forge
tar 1.35 h3b78370_0 conda-forge
tenacity 9.1.4 pyhcf101f3_0 conda-forge
tensordict 0.1.2 pyh6074d0b_0 conda-forge
throttler 1.2.2 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h366c992_103 conda-forge
toml 0.10.2 pyhcf101f3_3 conda-forge
tqdm 4.68.3 pyh8f84b5b_0 conda-forge
traitlets 5.15.1 pyhcf101f3_0 conda-forge
typing-extensions 4.15.0 h396c80c_0 conda-forge
typing_extensions 4.15.0 pyhcf101f3_0 conda-forge
tzdata 2025c hc9c84f9_1 conda-forge
urllib3 2.7.0 pyhd8ed1ab_0 conda-forge
vcflib 1.0.15 h3fa9d83_1 bioconda
wget 1.25.0 h653f8fd_1 conda-forge
wheel 0.47.0 pyhd8ed1ab_0 conda-forge
wrapt 1.17.0 py312h5eee18b_0 pkgs/main
wurlitzer 3.1.1 pyhd8ed1ab_1 conda-forge
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.6 he73a12e_0 conda-forge
xorg-libx11 1.8.13 he1eb515_0 conda-forge
xorg-libxau 1.0.12 hb03c661_1 conda-forge
xorg-libxdmcp 1.1.5 hb03c661_1 conda-forge
xorg-libxext 1.3.7 hb03c661_0 conda-forge
xorg-libxfixes 6.0.2 hb03c661_0 conda-forge
xorg-libxi 1.8.3 hb03c661_0 conda-forge
xorg-libxrandr 1.5.5 hb03c661_0 conda-forge
xorg-libxrender 0.9.12 hb9d3cd8_0 conda-forge
xorg-libxt 1.3.1 hb9d3cd8_0 conda-forge
xorg-libxtst 1.2.5 hb9d3cd8_3 conda-forge
yaml 0.2.5 h280c20c_3 conda-forge
yte 1.9.4 pyhd8ed1ab_0 conda-forge
zlib 1.3.2 h25fd6f3_2 conda-forge
zstd 1.5.7 hb78ec9c_6 conda-forge
</details>
erinyoung
reviewed
Jun 26, 2026
| grep "4b, 4d, 4e" lissero_test.tsv | ||
|
|
||
| RUN lissero --version && \ | ||
| blastn -version |
Contributor
There was a problem hiding this comment.
Can you add this line to the end of your file? micromamba list will list everything that was installed via micromamba and helps keep the tool-specific readme up-to-date.
RUN micromamba list -n base
Contributor
Author
|
Done, thanks @erinyoung. Added |
erinyoung
approved these changes
Jun 26, 2026
erinyoung
left a comment
erinyoung
left a comment
Contributor
There was a problem hiding this comment.
I have no additional changes to recommend. @Kincekara , did you have anything else?
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
3 participants
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.
Description
New container for LisSero 0.4.10, in silico serogroup typing for Listeria monocytogenes using the Doumith et al. 2004 multiplex-PCR scheme (five BLAST markers: prs, lmo0737, lmo1118, ORF2110, ORF2819). The marker database is bundled with the tool, so no external download is required.
mambaorg/micromamba:2.1.1-ubuntu22.04; lissero, BLAST+, procps-ng, and wget installed from bioconda/conda-forge.4b, 4d, 4eserogroup call, and checkslissero --versionandblastn -version.Built to the test target and validated via the fork's Manual test workflow.
Pull Request (PR) checklist:
build-files/lissero/0.4.10/Dockerfile)