-
Notifications
You must be signed in to change notification settings - Fork 126
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
update multiple GHActions workflows & new mlst update (#881)
* update multiple GHActions workflows to supress node.js warnings. lots of versions upgraded * more CI upgrades and a bugfix on the last variable reference * add dockerfile, readme, tests script for mlst with databases updated on 2024-03-08. also updated main readme. Not sure if it builds successfully yet * update test for novel allele which is no longer novel, and update dockerfile so that it builds successfully * update versions of github actions workflows used in the update_freyja workflow as well as the Test New Dockerfiles ghactions workflow * update readme to reflect date that the docker image will be built
- Loading branch information
Showing
9 changed files
with
229 additions
and
34 deletions.
There are no files selected for viewing
This file contains 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
This file contains 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
This file contains 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
This file contains 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
This file contains 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
This file contains 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
This file contains 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
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,109 @@ | ||
| FROM ubuntu:jammy as app | ||
|
|
||
| ARG MLST_VER="2.23.0" | ||
| ARG ANY2FASTA_VER="0.4.2" | ||
|
|
||
| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="mlst" | ||
| LABEL software.version="${MLST_VER}" | ||
| LABEL description="Scan contig files against PubMLST typing schemes" | ||
| LABEL website="https://github.com/tseemann/mlst" | ||
| LABEL license="https://github.com/tseemann/mlst/blob/master/LICENSE" | ||
| LABEL maintainer="Inês Mendes" | ||
| LABEL maintainer.email="[email protected]" | ||
| LABEL maintainer2="Curtis Kapsak" | ||
| LABEL maintainer2.email="[email protected]" | ||
|
|
||
| # install dependencies via apt; cleanup apt garbage | ||
| # blast from ubuntu:jammy is v2.12.0 (as of 2023-07-05) | ||
| # deps needed specifically for db download scripts: libfile-which-perl, curl, parallel | ||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| wget \ | ||
| ca-certificates \ | ||
| libmoo-perl \ | ||
| liblist-moreutils-perl \ | ||
| libjson-perl \ | ||
| gzip \ | ||
| file \ | ||
| ncbi-blast+ \ | ||
| libfile-which-perl \ | ||
| curl \ | ||
| parallel \ | ||
| procps && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
|
|
||
| # get any2fasta; move binary to /usr/local/bin which is already in $PATH | ||
| RUN wget https://github.com/tseemann/any2fasta/archive/refs/tags/v${ANY2FASTA_VER}.tar.gz && \ | ||
| tar xzf v${ANY2FASTA_VER}.tar.gz && \ | ||
| rm v${ANY2FASTA_VER}.tar.gz && \ | ||
| chmod +x any2fasta-${ANY2FASTA_VER}/any2fasta && \ | ||
| mv -v any2fasta-${ANY2FASTA_VER}/any2fasta /usr/local/bin | ||
|
|
||
| # get mlst | ||
| RUN wget https://github.com/tseemann/mlst/archive/v${MLST_VER}.tar.gz && \ | ||
| tar -xzf v${MLST_VER}.tar.gz && \ | ||
| rm -v v${MLST_VER}.tar.gz | ||
|
|
||
| # set PATH and perl local settings | ||
| ENV PATH="${PATH}:/mlst-${MLST_VER}/bin:" \ | ||
| LC_ALL=C.UTF-8 | ||
|
|
||
| # check dependencies and list available schemes | ||
| RUN mlst --check && mlst --list | ||
|
|
||
| # update databases, following steps from here, but modified after much trial and error: https://github.com/tseemann/mlst#updating-the-database | ||
| # delete the old databases instead of renaming & saving the dir | ||
| RUN cd /mlst-${MLST_VER}/scripts && \ | ||
| mkdir -v db-downloaded-$(date -I) && \ | ||
| ./mlst-download_pub_mlst -d db-downloaded-$(date -I) | bash && \ | ||
| rm -rv /mlst-${MLST_VER}/db/pubmlst && \ | ||
| mv -v db-downloaded-$(date -I) /mlst-${MLST_VER}/db/pubmlst && \ | ||
| ./mlst-make_blast_db && \ | ||
| mlst --list | ||
|
|
||
| WORKDIR /data | ||
|
|
||
| # default command is to pull up help options; can be overridden of course | ||
| CMD ["mlst", "--help"] | ||
|
|
||
| ### start of test stage ### | ||
| # using app stage as base image for test stage | ||
| FROM app as test | ||
|
|
||
| # copy in test script; run script | ||
| # test commands stolen shamelessly from https://github.com/tseemann/mlst/blob/master/.travis.yml | ||
| COPY mlst-tests.sh . | ||
| RUN bash mlst-tests.sh | ||
|
|
||
| # need unzip for the datasets tool | ||
| RUN apt-get update && apt-get install -y --no-install-recommends unzip | ||
|
|
||
| # for pinning the version of NCBI datasets that is downloaded for this test | ||
| ARG DATASETS_VER="16.2.0" | ||
|
|
||
| # install ncbi datasets tool (pre-compiled binary) | ||
| RUN wget https://github.com/ncbi/datasets/releases/download/v${DATASETS_VER}/linux-amd64.cli.package.zip && \ | ||
| unzip linux-amd64.cli.package.zip && \ | ||
| rm linux-amd64.cli.package.zip && \ | ||
| chmod +x dataformat datasets | ||
|
|
||
| # downloading an E. coli (from CT) with a known newer sequence type ST15199 which was designated on 2023-10-16 | ||
| # MLST scheme info here (from Enterobase): https://pubmlst.org/bigsdb?page=profileInfo&db=pubmlst_escherichia_seqdef&scheme_id=1&profile_id=15199 | ||
| # E. coli genome: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_032604515.1/ | ||
| # BioSample: SAMN37796909 | ||
| ARG GENBANK_ACCESSION="GCA_032604515.1" | ||
| RUN datasets download genome accession ${GENBANK_ACCESSION} --filename ${GENBANK_ACCESSION}.zip && \ | ||
| mkdir -v ${GENBANK_ACCESSION}-download && \ | ||
| unzip ${GENBANK_ACCESSION}.zip -d ${GENBANK_ACCESSION}-download && \ | ||
| rm -v ${GENBANK_ACCESSION}.zip && \ | ||
| mv -v ${GENBANK_ACCESSION}-download/ncbi_dataset/data/${GENBANK_ACCESSION}/${GENBANK_ACCESSION}*.fna ${GENBANK_ACCESSION}-download/ncbi_dataset/data/${GENBANK_ACCESSION}/${GENBANK_ACCESSION}.genomic.fna && \ | ||
| mlst ${GENBANK_ACCESSION}-download/ncbi_dataset/data/${GENBANK_ACCESSION}/${GENBANK_ACCESSION}.genomic.fna | tee mlst.${GENBANK_ACCESSION}.tsv && \ | ||
| echo && \ | ||
| echo "Checking for ST15199 in the mlst results now..." && \ | ||
| grep "15199" mlst.${GENBANK_ACCESSION}.tsv | ||
|
|
||
| ### Example command to run mlst (broken into two lines for readability) | ||
| ### If you have an assembly named contigs.fasta in your PWD: | ||
| # $ docker run -v ${PWD}:/data staphb/mlst:latest \ | ||
| # mlst contigs.fasta >mlst-results.tsv |
Oops, something went wrong.