Add pangolin 4.4 with pangolin-data 1.39

[kapsakcj]

Draft for now. Docker image builds successfully. Need to update LABELS.

Ready for review.

LABELs have been updated to match those listed in PR https://github.com/StaPH-B/docker-builds/pull/1651/changes

The main change is upgrade to pangolin-data v1.39. I have added an additional test for a lineage (XFG.6.14) defined in 1.39

Also upgraded the micromamba base image to the latest version 2.8.1

GHActions test started failing after I updated the LABELs to the OCI spec. Should be OK to merge regardless - the image builds and tests run successfully

Pull Request (PR) checklist:

• Include a description of what is in this pull request in this message.
• The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/build-files/samtools/1.15 )
• Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number in build-files (i.e. docker-builds/build-files/spades/3.12.0/Dockerfile)
  • (optional) All test files are located in same directory as the Dockerfile (i.e. build-files/shigatyper/2.0.1/test.sh)
• Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. docker-builds/build-files/spades/3.12.0/README.md)
  • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
• Dockerfile includes the recommended LABELS
• Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

[kapsakcj]

@staphb-dockerbuilds-diff pangolin 4.4-pdata-1.39 4.4-pdata-1.38

[github-actions]

Dockerfile Diff: pangolin

Comparing: 4.4-pdata-1.39 -> 4.4-pdata-1.38

--- build-files/pangolin/4.4-pdata-1.39/Dockerfile	2026-06-10 17:52:25.893776613 +0000
+++ build-files/pangolin/4.4-pdata-1.38/Dockerfile	2026-06-10 17:52:25.893511575 +0000
@@ -1,4 +1,4 @@
-FROM mambaorg/micromamba:2.8.1-ubuntu24.04 AS app
+FROM mambaorg/micromamba:2.5.0-ubuntu24.04 AS app
 
 # build and run as root users since micromamba image has 'mambauser' set as the $USER
 USER root
@@ -9,31 +9,22 @@
 # had to include the v for some of these due to GitHub tags.
 # using pangolin-data github tag, NOT what is in the GH release title "v1.2.133"
 ARG PANGOLIN_VER="v4.4"
-ARG PANGOLIN_DATA_VER="v1.39"
+ARG PANGOLIN_DATA_VER="v1.38"
 ARG SCORPIO_VER="v0.3.19"
 ARG CONSTELLATIONS_VER="v0.1.12"
 ARG USHER_VER="0.6.3"
 
-# metadata labels for the image; using OCI labels spec:
-LABEL \
-# The exact base image used for the 'app' stage
-org.opencontainers.image.base.name="mambaorg/micromamba:2.8.1-ubuntu24.04" \
-# The name of the software (e.g., "BWA" or "Samtools")
-org.opencontainers.image.title="pangolin" \
-# The version of the software itself
-org.opencontainers.image.version="${PANGOLIN_VER}" \
-# The version of THIS Dockerfile (increment if you change the build logic)
-org.opencontainers.image.revision="1" \
-# A human-readable description of the tool
-org.opencontainers.image.description="Conda environment for Pangolin. Pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages." \
-# The project homepage or GitHub repository
-org.opencontainers.image.url="https://github.com/cov-lineages/pangolin" \
-# Where users can find instructions or manuals for the software
-org.opencontainers.image.documentation="https://github.com/cov-lineages/pangolin" \
-# The software license (e.g., MIT, GPL-3.0, Apache-2.0) for the software
-org.opencontainers.image.licenses="GPL-3.0" \
-# The person/group maintaining this Dockerfile
-org.opencontainers.image.authors="Curtis Kapsak <kapsakcj@gmail.com>"
+# metadata labels
+LABEL base.image="mambaorg/micromamba:2.5.0-ubuntu24.04"
+LABEL dockerfile.version="1"
+LABEL software="pangolin"
+LABEL software.version=${PANGOLIN_VER}
+LABEL description="Conda environment for Pangolin. Pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages."
+LABEL website="https://github.com/cov-lineages/pangolin"
+LABEL license="GNU General Public License v3.0"
+LABEL license.url="https://github.com/cov-lineages/pangolin/blob/master/LICENSE.txt"
+LABEL maintainer="Curtis Kapsak"
+LABEL maintainer.email="kapsakcj@gmail.com"
 
 # install dependencies; cleanup apt garbage
 RUN apt-get update && apt-get install -y --no-install-recommends \
@@ -133,9 +124,8 @@
 # XFG.3.5 | PX025687.1 | introduced in pango-designation 1.35 https://github.com/cov-lineages/pango-designation/commit/cb430033b29f760b7f013ff7114790c5b4b6f9b4
 # XFG.5.1.4 | PV979512.1 | introduced in pango-designation 1.36 https://github.com/cov-lineages/pango-designation/commit/9bc6a238df1bcda12f548b239a86c7ce7fbcf2a3
 # PQ.17.11 | PX697933.1 | introduced in pango-designation 1.37 https://github.com/cov-lineages/pango-designation/commit/38e4ffc100689e8979c786623e62a1d2887f46e9
-# XFG.6.14 | PX670354.1 | introduced in pango-designation 1.39 https://github.com/cov-lineages/pango-designation/commit/2079448d187e4f5308953a529cb24936723eeeac
 # sed is to make output more readable by removing extra text in sequence names
-RUN datasets download virus genome accession ON924087.1,OQ381818.1,OR177999.1,OR461132.1,OR598183.1,OR716684.1,PP189069.1,PP218754.1,PQ073669.1,PP770375.1,PQ034842.1,PQ277908.1,PQ725776.1,PV666687.1,PX025687.1,PV979512.1,PX697933.1,PX670354.1 && \
+RUN datasets download virus genome accession ON924087.1,OQ381818.1,OR177999.1,OR461132.1,OR598183.1,OR716684.1,PP189069.1,PP218754.1,PQ073669.1,PP770375.1,PQ034842.1,PQ277908.1,PQ725776.1,PV666687.1,PX025687.1,PV979512.1,PX697933.1 && \
 unzip -o ncbi_dataset.zip && \
 rm -v ncbi_dataset.zip && \
 pangolin ncbi_dataset/data/genomic.fna && \

[erinyoung]

New labels!

The following are intended to be added by the "deploy" github action in #1652, and so are not included in the template.

org.opencontainers.image.created={{date 'YYYY-MM-DDTHH:mm:ssZ'}}
org.opencontainers.image.source=https://github.com/StaPH-B/docker-builds/${{ inputs.tool }}/${{ inputs.docker_image_tag }}

I will add these tomorrow and get this deployed and merged.

[erinyoung]

Tests worked

#15 24.65 Output file written to: /data/test_seqs-output-pusher/lineage_report.csv
#15 24.79 taxon                                lineage     conflict  ambiguity_score  scorpio_call          scorpio_support  scorpio_conflict  scorpio_notes                                                              version       pangolin_version  scorpio_version  constellation_version  is_designated  qc_status  qc_notes                note
#15 24.79 India seq                            B.1.617.1   0.0                        B.1.617.1-like        1.0              0.0               scorpio call: Alt alleles 11; Ref alleles 0; Amb alleles 0; Oth alleles 0  PUSHER-v1.39  4.4               0.3.19           v0.1.12                False          pass       Ambiguous_content:0.02  Usher placements: B.1.617.1(1/1)
#15 24.79 b117                                 B.1.1.7     0.0                        Alpha (B.1.1.7-like)  0.91             0.04              scorpio call: Alt alleles 21; Ref alleles 1; Amb alleles 1; Oth alleles 0  PUSHER-v1.39  4.4               0.3.19           v0.1.12                False          pass       Ambiguous_content:0.02  Usher placements: B.1.1.7(2/2)
#15 24.79 outgroup_A                           A           0.0                                                                                                                                                            PUSHER-v1.39  4.4               0.3.19           v0.1.12                False          pass       Ambiguous_content:0.02  Usher placements: A(1/1)
#15 24.79 issue_57_torsten_seq                 Unassigned                                                                                                                                                                 PUSHER-v1.39  4.4               0.3.19           v0.1.12                False          fail       failed to map           
#15 24.79 This_seq_has_6000_Ns_in_18000_bases  Unassigned                                                                                                                                                                 PUSHER-v1.39  4.4               0.3.19           v0.1.12                False          fail       failed to map           
#15 24.79 This_seq_has_no_seq                  Unassigned                                                                                                                                                                 PUSHER-v1.39  4.4               0.3.19           v0.1.12                False          fail       failed to map           
#15 24.79 This_seq_is_too_short                Unassigned                                                                                                                                                                 PUSHER-v1.39  4.4               0.3.19           v0.1.12                False          fail       Ambiguous_content:0.9   
#15 24.79 This_seq_has_lots_of_Ns              Unassigned                                                                                                                                                                 PUSHER-v1.39  4.4               0.3.19           v0.1.12                False          fail       Ambiguous_content:0.98  
#15 24.79 This_seq_is_literally_just_N         Unassigned                                                                                                                                                                 PUSHER-v1.39  4.4               0.3.19           v0.1.12                False          fail       failed to map           
#15 24.79 Japan_seq                            B           0.0                                                                                                                                                            PANGO-v1.39   4.4               0.3.19           v0.1.12                True           pass       Ambiguous_content:0.02  Assigned from designation hash.
#15 24.79 USA_seq                              B.1.314     0.0                                                                                                                                                            PANGO-v1.39   4.4               0.3.19           v0.1.12                True           pass       Ambiguous_content:0.02  Assigned from designation hash.
#15 24.79 Unassigned_omicron_seq               BA.1        0.0                        Omicron (BA.1-like)   0.71             0.09              scorpio call: Alt alleles 41; Ref alleles 5; Amb alleles 9; Oth alleles 3  PUSHER-v1.39  4.4               0.3.19           v0.1.12                False          pass       Ambiguous_content:0.03  Usher placements: BA.1(1/1)
#15 DONE 24.8s

[erinyoung]

The labels cause the github actions to fail, but this is otherwise a functional image. I will approve and get this merged.

[kapsakcj]

thank you for adding those labels and reviewing!

[erinyoung]

Thank you for putting this together! You can check the status of the deploy here : https://github.com/StaPH-B/docker-builds/actions/runs/27360846336