adds pangolin 4.3.1 with new pdata 1.30

kapsakcj commented 3 weeks ago

Changes from previous dockerfile

updating to pangolin-data & pangolin-assignement 1.30
upgraded base image to latest micromamba-docker version
added unzip -o option to overwrite files named the same (like md5sum.txt that comes with genomes downloaded using ncbi datasets). These files are unnecessary to keep around so I just opted to overwrite them each time a .zip file is unzipped & files are extracted.
added test for new lineage, MC.2

code diff:

$ diff pangolin/4.3.1-pdata-1.29/Dockerfile pangolin/4.3.1-pdata-1.30/Dockerfile 
1c1
< FROM mambaorg/micromamba:1.5.8 AS app
---
> FROM mambaorg/micromamba:1.5.10 AS app
12c12
< ARG PANGOLIN_DATA_VER="v1.29"
---
> ARG PANGOLIN_DATA_VER="v1.30"
18c18
< LABEL base.image="mambaorg/micromamba:1.5.8"
---
> LABEL base.image="mambaorg/micromamba:1.5.10"
126c126
<  unzip OQ381818.1.zip && rm OQ381818.1.zip && \
---
>  unzip -o OQ381818.1.zip && rm OQ381818.1.zip && \
135c135
< unzip OR177999.1.zip && rm OR177999.1.zip && \
---
> unzip -o OR177999.1.zip && rm OR177999.1.zip && \
144c144
< unzip OR461132.1.zip && rm OR461132.1.zip && \
---
> unzip -o OR461132.1.zip && rm OR461132.1.zip && \
153c153
< unzip OR598183.1.zip && rm OR598183.1.zip && \
---
> unzip -o OR598183.1.zip && rm OR598183.1.zip && \
164c164
< unzip OR716684.1.zip && rm OR716684.1.zip && \
---
> unzip -o OR716684.1.zip && rm OR716684.1.zip && \
174c174
< unzip PP189069.1.zip && rm PP189069.1.zip && \
---
> unzip -o PP189069.1.zip && rm PP189069.1.zip && \
185c185
< unzip PP218754.1.zip && rm PP218754.1.zip && \
---
> unzip -o PP218754.1.zip && rm PP218754.1.zip && \
195c195
< unzip PP770375.1.zip && rm PP770375.1.zip && \
---
> unzip -o PP770375.1.zip && rm PP770375.1.zip && \
204c204
< unzip PQ073669.1.zip && rm PQ073669.1.zip && \
---
> unzip -o PQ073669.1.zip && rm PQ073669.1.zip && \
208c208,217
< column -t -s, PQ073669.1-usher/lineage_report.csv
\ No newline at end of file
---
> column -t -s, PQ073669.1-usher/lineage_report.csv
> 
> # new lineage MC.2 that was introduced in pango-designation v1.30: https://github.com/cov-lineages/pango-designation/commit/c64dbc47fbfbfd7f4da011deeb1a88dd6baa45f1#diff-a121ea4b8cbeb4c0020511b5535bf24489f0223cc83511df7b8209953115d329R2564181
> # genome on NCBI: https://www.ncbi.nlm.nih.gov/nuccore/PQ034842.1
> RUN datasets download virus genome accession PQ034842.1 --filename PQ034842.1.zip && \
> unzip -o PQ034842.1.zip && rm PQ034842.1.zip && \
> mv -v ncbi_dataset/data/genomic.fna PQ034842.1.genomic.fna && \
> rm -vr ncbi_dataset/ README.md && \
> pangolin PQ034842.1.genomic.fna -o PQ034842.1-usher && \
> column -t -s, PQ034842.1-usher/lineage_report.csv

Pull Request (PR) checklist:

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

kapsakcj commented 3 weeks ago

Does anyone have the bandwidth to review this PR?

erinyoung commented 3 weeks ago

It looks like the tests work.

#19 [test  7/17] RUN datasets download virus genome accession ON924087.1 --filename ON924087.1.zip &&  unzip ON924087.1.zip && rm ON924087.1.zip &&  mv -v ncbi_dataset/data/genomic.fna ON924087.1.genomic.fna &&  rm -vr ncbi_dataset/ README.md &&  pangolin ON924087.1.genomic.fna -o ON924087.1-usher &&  column -t -s, ON924087.1-usher/lineage_report.csv
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#29 12.88 ****
#29 12.88 Data files found:
#29 12.88 usher_pb: /opt/conda/envs/pangolin/lib/python3.8/site-packages/pangolin_data/data/lineageTree.pb
#29 12.88 ****
#29 12.88 ****
#29 12.88 Output file written to: /data/PQ034842.1-usher/lineage_report.csv
#29 12.99 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                    
#29 12.99 "PQ034842.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/NY-CDC-LC1108001/2024   complete genome"  MC.2      0.0                            Omicron (BA.2-like)  0.92              0.02           scorpio call: Alt alleles 57; Ref alleles 1; Amb alleles 0; Oth alleles 4  PANGO-v1.30       4.3.1            0.3.19                 v0.1.12        True       pass      Ambiguous_content:0.02  Assigned from designation hash.
#29 DONE 13.0s

erinyoung commented 3 weeks ago

Thank you for putting this together!

I'm going to deploy this to dockerhub and quay to staphb/pangolin using the tags '4.3.1-pdata-1.30' and 'latest'

StaPH-B / docker-builds

adds pangolin 4.3.1 with new pdata 1.30 #1052