Add mash 2.3 container with refreshed RefSeq prokaryotic sketch (v235)#1717
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Add build-files/mash/2.3-RefSeqProkv235 — Mash 2.3 bundled with the v235 RefSeq prokaryotic reference sketch (Zenodo 10.5281/zenodo.20293962), replacing the 2019 RefSeqSketchesDefaults.msh. The reference sketch is generated and published by Erin Young's update_mash_dist pipeline (https://github.com/erinyoung/update_mash_dist), which regenerates the RefSeq sketch after each RefSeq release. Includes app/test stages; updates the README image table.
Collaborator
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@arodzh-sudo Thank you for your PR. |
Contributor
Author
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Thanks @Kincekara. Switched the base image to ubuntu:noble in a39dfe9 |
Contributor
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@staphb-dockerbuilds-diff mash 2.3 2.3-RefSeqProkv235 |
Dockerfile Diff: mashComparing: 2.3 -> 2.3-RefSeqProkv235 --- build-files/mash/2.3/Dockerfile 2026-06-26 18:43:07.707090277 +0000
+++ build-files/mash/2.3-RefSeqProkv235/Dockerfile 2026-06-26 18:43:07.706975884 +0000
@@ -1,38 +1,55 @@
-FROM ubuntu:xenial
+FROM ubuntu:noble AS app
-# for easy upgrade later. ARG variables only persist during image build time
-ARG MASH_VER="2.3"
+ARG MASH_VER="v2.3"
+ARG SKETCH_VER="235"
-LABEL base.image="ubuntu:xenial"
+LABEL base.image="ubuntu:noble"
LABEL dockerfile.version="1"
LABEL software="Mash"
LABEL software.version="2.3"
-LABEL description="Fast genome and metagenome distance estimation using MinHash"
-LABEL website="https://mash.readthedocs.io/en/latest/index.html"
+LABEL description="Fast genome/metagenome distance estimation (MinHash), bundled with a refreshed RefSeq prokaryotic reference sketch (v235, Zenodo 10.5281/zenodo.20293962)"
+LABEL website="https://github.com/marbl/Mash"
LABEL license="https://github.com/marbl/Mash/blob/master/LICENSE.txt"
-LABEL maintainer="Curtis Kapsak"
-LABEL maintainer.email="pjx8@cdc.gov"
+LABEL maintainer="Arnold Rodriguez"
+LABEL maintainer.email="arnold.rodriguezhilario@flhealth.gov"
-# install dependencies
-RUN apt-get update && apt-get -y install \
- wget && \
- apt-get autoclean && \
- rm -rf /var/lib/apt/lists/*
-
-# download mash binary; make /data
-RUN wget https://github.com/marbl/Mash/releases/download/v${MASH_VER}/mash-Linux64-v${MASH_VER}.tar && \
- tar -xvf mash-Linux64-v${MASH_VER}.tar && \
- rm -rf mash-Linux64-v${MASH_VER}.tar && \
- mkdir /data
-
-# add mash to path, and set perl locale settings
-ENV PATH="${PATH}:/mash-Linux64-v${MASH_VER}" \
- LC_ALL=C
+RUN apt-get update && apt-get install --no-install-recommends -y \
+ wget \
+ ca-certificates \
+ procps && \
+ apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# install mash 2.3 precompiled linux64 binary
+RUN wget https://github.com/marbl/Mash/releases/download/${MASH_VER}/mash-Linux64-${MASH_VER}.tar && \
+ tar -xvf mash-Linux64-${MASH_VER}.tar --no-same-owner && \
+ rm mash-Linux64-${MASH_VER}.tar && \
+ mv /mash-Linux64-${MASH_VER}/mash /usr/local/bin/ && \
+ mkdir /data
+
+# refreshed RefSeq prokaryotic sketch, embedded at build time (verify MD5 before gunzip)
+RUN mkdir /db && cd /db && \
+ wget -O RefSeqProkSketchesv${SKETCH_VER}.msh.gz \
+ "https://zenodo.org/records/20293962/files/RefSeqSketches_${SKETCH_VER}.msh.gz?download=1" && \
+ echo "2885e98f2d985b2b4f8f8ce9978040d2 RefSeqProkSketchesv${SKETCH_VER}.msh.gz" | md5sum -c - && \
+ gunzip RefSeqProkSketchesv${SKETCH_VER}.msh.gz
+
+ENV LC_ALL=C
+
+CMD ["/bin/bash", "-c", "mash -h && echo '** RefSeq prokaryotic reference sketch (v235) is located at /db/RefSeqProkSketchesv235.msh'"]
WORKDIR /data
-# make db dir. Store db there. Better to have db's added in the last layers
-RUN mkdir /db && \
- cd /db && \
- wget https://gembox.cbcb.umd.edu/mash/RefSeqSketchesDefaults.msh.gz && \
- gunzip RefSeqSketchesDefaults.msh.gz
+FROM app AS test
+
+ARG SKETCH_VER="235"
+
+# verify tool and reference sketch integrity
+WORKDIR /db
+RUN mash --version && mash -h && \
+ mash info RefSeqProkSketchesv${SKETCH_VER}.msh | head -n 10
+
+# functional test: Enterobacter hormaechei FDAARGOS_1433 (ECC) screened against the refreshed sketch
+WORKDIR /test
+RUN wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/019/048/245/GCF_019048245.1_ASM1904824v1/GCF_019048245.1_ASM1904824v1_genomic.fna.gz && \
+ gunzip GCF_019048245.1_ASM1904824v1_genomic.fna.gz && \
+ mash screen -p 4 /db/RefSeqProkSketchesv${SKETCH_VER}.msh GCF_019048245.1_ASM1904824v1_genomic.fna | sort -gr | head |
Contributor
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Test worked |
erinyoung
reviewed
Jun 26, 2026
Comment on lines
+20
to
+24
| The sketch replaces the 2019 `RefSeqSketchesDefaults.msh` distributed with `staphb/mash:2.3`. It is regenerated from RefSeq representative bacterial genomes by Erin Young's [`update_mash_dist`](https://github.com/erinyoung/update_mash_dist) pipeline (Mash 2.3, default k=21 / s=1000) and published to Zenodo: | ||
| - Version: v235 (published 2026-05-19) | ||
| - Zenodo record: 20293962 | ||
| - DOI: [10.5281/zenodo.20293962](https://doi.org/10.5281/zenodo.20293962) | ||
| - Source file: `RefSeqSketches_235.msh.gz` (MD5 `2885e98f2d985b2b4f8f8ce9978040d2`) |
Contributor
There was a problem hiding this comment.
Thank you for including this!
erinyoung
approved these changes
Jun 26, 2026
erinyoung
left a comment
erinyoung
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I have no changes to recommend.
I am going to approve this PR and get this deployed to dockerhub and quay using the tag '2.3-RefSeqProkv235'. I will not be overwriting the 'latest' tag for staphb/mash
Contributor
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Thank you for putting this together! You can check the status of the deploy here : https://github.com/StaPH-B/docker-builds/actions/runs/28258766636 |
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Description
Adds a new Mash container variant,
staphb/mash:2.3-RefSeqProkv235, that embeds a refreshed RefSeq prokaryotic reference sketch (v235) in place of the 2019RefSeqSketchesDefaults.mshincluded instaphb/mash:2.3.Why: the 2019 sketch under-represents recent type strains and contributes to Enterobacter cloacae complex (ECC) mis-calls. The v235 sketch is regenerated from RefSeq representative bacterial genomes (Mash 2.3, k=21, s=1000) and refreshes the candidate pool.
The sketch is downloaded from Zenodo and MD5-verified at build time, then stored at
/db/RefSeqProkSketchesv235.msh:RefSeqSketches_235.msh.gz, MD52885e98f2d985b2b4f8f8ce9978040d2The reference sketch is generated and published by Erin Young's
update_mash_distpipeline.Testing (via the "Manual test" Action, build to the
testtarget):mash infoconfirms k=21 and 22,274 sketchesmash screenof E. hormaechei FDAARGOS_1433 returns it at identity 1.0, with the remaining ECC species ranked directly belowPull Request (PR) checklist:
docker build --tag mash:2.3-RefSeqProkv235test --target test build-files/mash/2.3-RefSeqProkv235) — verified via the "Manual test" GitHub Action.build-files/mash/2.3-RefSeqProkv235/Dockerfile).teststage (no separatetest.sh).