Merge pull request #1575 from cwoodside1278/jasmine-26.1.2

Update pbjasmine to 26.1.2

Author: erinyoung

README.md

@@ -205,7 +205,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [IRMA](https://hub.docker.com/r/staphb/irma/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/irma)](https://hub.docker.com/r/staphb/irma) | <details><summary>Click to see all versions</summary> <ul><li>[1.0.2](./build-files/irma/1.0.2/)</li><li>[1.0.3](./build-files/irma/1.0.3/)</li><li>[1.1.2](./build-files/irma/1.1.2/)</li><li>[1.1.3](./build-files/irma/1.1.3/)</li><li>[1.1.4](./build-files/irma/1.1.4/)</li><li>[1.2.0](./build-files/irma/1.2.0/)</li><li>[1.3.0](./build-files/irma/1.3.0/)</li><li>[1.3.1](./build-files/irma/1.3.1/)</li></ul> </details> | <li>https://wonder.cdc.gov/amd/flu/irma/</li><li>https://github.com/CDCgov/irma</li>|
 | [isPcr](https://users.soe.ucsc.edu/~kent/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ispcr)](https://hub.docker.com/r/staphb/ispcr) | <details><summary>Click to see all versions</summary> <ul><li>[33](./build-files/ispcr/33/)</li></ul> </details> | https://users.soe.ucsc.edu/~kent/ |
 | [iVar](https://hub.docker.com/r/staphb/ivar/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ivar)](https://hub.docker.com/r/staphb/ivar) | <details><summary>Click to see all versions</summary> <ul><li>[1.1](./build-files/ivar/1.1/)</li><li>[1.1 (+SARS-CoV2 reference)](./build-files/ivar/1.1-SC2/)</li><li>[1.2.1](./build-files/ivar/1.2.1/)</li><li>[1.2.1 (+SC2 ref)](./build-files/ivar/1.2.1-SC2/)</li><li>[1.2.2 (+SC2 ref and artic bedfiles)](./build-files/ivar/1.2.2_artic20200528/)</li><li>[1.3](./build-files/ivar/1.3/)</li><li>[1.3.1](./build-files/ivar/1.3.1/)</li><li>[1.3.2](./build-files/ivar/1.3.2/)</li><li>[1.4.1](./build-files/ivar/1.4.1/)</li><li>[1.4.2](./build-files/ivar/1.4.2/)</li><li>[1.4.3](./build-files/ivar/1.4.3/)</li><li>[1.4.4](./build-files/ivar/1.4.4/)</li><li>[1.4.4-aligners (+bwa and minimap2)](./build-files/ivar/1.4.4-aligners/)</li></ul> </details> | https://github.com/andersen-lab/ivar |
-| [Jasmine](https://hub.docker.com/r/staphb/pbjasmine/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pbjasmine)](https://hub.docker.com/r/staphb/pbjasmine) | <details><summary>Click to see all versions</summary> <ul><li>[2.0.0](./build-files/pbjasmine/2.0.0/)</li><li>[2.4.0](./build-files/pbjasmine/2.4.0/)</li></ul> </details> | https://github.com/PacificBiosciences/jasmine |
+| [Jasmine](https://hub.docker.com/r/staphb/pbjasmine/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pbjasmine)](https://hub.docker.com/r/staphb/pbjasmine) | <details><summary>Click to see all versions</summary> <ul><li>[2.0.0](./build-files/pbjasmine/2.0.0/)</li><li>[2.4.0](./build-files/pbjasmine/2.4.0/)</li><li>[26.1.2](./build-files/pbjasmine/26.1.2/)</li></ul> </details> | https://github.com/PacificBiosciences/jasmine |
 | [Kaptive](https://hub.docker.com/r/staphb/kaptive/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/kaptive)](https://hub.docker.com/r/staphb/kaptive) | <details><summary>Click to see all versions</summary> <ul><li>[2.0.0](./build-files/kaptive/2.0.0/)</li><li>[2.0.3](./build-files/kaptive/2.0.3/)</li><li>[2.0.5](./build-files/kaptive/2.0.5/)</li><li>[2.0.8](./build-files/kaptive/2.0.8/)</li><li>[3.0.0b6](./build-files/kaptive/3.0.0b6/)</li><li>[3.1.0](./build-files/kaptive/3.1.0/)</li></ul> </details> | https://github.com/klebgenomics/Kaptive |
 | [Kleborate](https://hub.docker.com/r/staphb/kleborate/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/kleborate)](https://hub.docker.com/r/staphb/kleborate) | <details><summary>Click to see all versions</summary> <ul><li>[2.0.4](./build-files/kleborate/2.0.4/)</li><li>[2.1.0](./build-files/kleborate/2.1.0/)</li><li>[2.2.0](./build-files/kleborate/2.2.0/)</li><li>[2.3.2](./build-files/kleborate/2.3.2)</li><li>[2.3.2-2023-05](./build-files/kleborate/2.3.2-2023-05/)</li><li>[2.4.1](./build-files/kleborate/2.4.1/)</li><li>[3.1.2](./build-files/kleborate/3.1.2/)</li><li>[3.1.3](./build-files/kleborate/3.1.3/)</li><li>[3.2.4](./build-files/kleborate/3.2.4/)</li><li>[3.2.4-micromamba](./build-files/kleborate/3.2.4-micromamba/)</li></ul> </details> | https://github.com/klebgenomics/Kleborate <br/> https://github.com/klebgenomics/Kaptive |
 | [kma](https://hub.docker.com/r/staphb/kma/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/kma)](https://hub.docker.com/r/staphb/kma) | <details><summary>Click to see all versions</summary> <ul><li>[1.2.21](./build-files/kma/1.2.21/)</li><li>[1.4.10 (no database)](./build-files/kma/1.4.10/)</li><li>[1.4.14](./build-files/kma/1.4.14/) (no database)</li><li>[1.4.17](./build-files/kma/1.4.17/) (no database)</li><li>[1.5.2](./build-files/kma/1.5.2/) (no database)</li><li>[1.6.4](./build-files/kma/1.6.4/)</li><</ul> </details> | https://bitbucket.org/genomicepidemiology/kma/ |

build-files/pbjasmine/26.1.2/Dockerfile

@@ -0,0 +1,43 @@
+FROM ubuntu:noble AS app
+
+ARG JASMINE_VER="26.1.2"
+
+LABEL base.image="ubuntu:noble"
+LABEL dockerfile.version="1"
+LABEL software="Jasmine"
+LABEL software.version="${JASMINE_VER}"
+LABEL description="Jasmine predicts 5-Methylcytosine (5mC) of each CpG site in PacBio HiFi reads"
+LABEL website="https://github.com/pacificbiosciences/jasmine/"
+LABEL license="https://github.com/PacificBiosciences/jasmine/blob/main/LICENSE"
+LABEL maintainer="Kutluhan Incekara"
+LABEL maintainer.email="kutluhan.incekara@ct.gov"
+
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    wget \
+    xz-utils &&\
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN wget --no-check-certificate https://github.com/PacificBiosciences/jasmine/releases/download/v${JASMINE_VER}/jasmine.tar.xz &&\
+    tar -C /usr/local/ -xvf jasmine.tar.xz &&\
+    rm jasmine.tar.xz    
+
+ENV LC_ALL=C
+
+CMD [ "jasmine", "-h" ]
+
+WORKDIR /data
+
+## Test prep ##
+FROM staphb/pbtk:3.1.1 AS testdata
+
+RUN wget -q --no-check-certificate https://downloads.pacbcloud.com/public/Sequel-II-CpG-training/CCS/methylated/m64168_200823_191315.hifi_reads.bam &&\
+    pbindex m64168_200823_191315.hifi_reads.bam &&\
+    zmwfilter --downsample-count 10 m64168_200823_191315.hifi_reads.bam test.bam &&\
+    rm m64168_200823_191315.hifi_reads.bam
+
+## Test ##
+FROM app AS test
+
+COPY --from=testdata /data/test.bam /data/test.bam 
+
+RUN jasmine test.bam out.bam --log-level INFO

build-files/pbjasmine/26.1.2/README.md

@@ -0,0 +1,24 @@
+# Jasmine container
+
+Main tool: [jasmine](https://github.com/PacificBiosciences/jasmine)
+  
+Code repository: https://github.com/PacificBiosciences/jasmine
+
+Additional tools:
+
+Basic information on how to use this tool:
+
+- executable: jasmine
+- help: -h, --help
+- version: --version
+- description: Jasmine predicts 5-Methylcytosine (5mC) of each CpG site in PacBio HiFi reads.
+
+Additional information:
+
+Full documentation: https://github.com/PacificBiosciences/jasmine
+
+## Example Usage
+
+```bash
+jasmine movie.hifi_reads.bam movie.5mc.hifi_reads.bam
+```