adding samtools version 1.21

Author: erinyoung

README.md

@@ -124,7 +124,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [bakta](https://hub.docker.com/r/staphb/bakta) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bakta)](https://hub.docker.com/r/staphb/bakta) | <ul><li>[1.9.2](./bakta/1.9.2/)</li><li>[1.9.2-light](./bakta/1.9.2-5.1-light/)</li><li>[1.9.3](./bakta/1.9.3/)</li><li>[1.9.3-light](./bakta/1.9.3-5.1-light/)</li><li>[1.9.4](./bakta/1.9.4/)</li></ul> | https://github.com/oschwengers/bakta |
 | [bandage](https://hub.docker.com/r/staphb/bandage) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bandage)](https://hub.docker.com/r/staphb/bandage) | <ul><li>[0.8.1](./bandage/0.8.1/)</li></ul> | https://rrwick.github.io/Bandage/ |
 | [BBTools](https://hub.docker.com/r/staphb/bbtools/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bbtools)](https://hub.docker.com/r/staphb/bbtools) | <ul><li>[38.76](./bbtools/38.76/)</li><li>[38.86](./bbtools/38.86/)</li><li>[38.95](./bbtools/38.95/)</li><li>[38.96](./bbtools/38.96/)</li><li>[38.97](./bbtools/38.97/)</li><li>[38.98](./bbtools/38.98/)</li><li>[38.99](./bbtools/38.99/)</li><li>[39.00](./bbtools/39.00/)</li><li>[39.01](./bbtools/39.01/)</li><li>[39.06](./bbtools/39.06/)</li></ul> | https://jgi.doe.gov/data-and-tools/bbtools/ |
-| [bcftools](https://hub.docker.com/r/staphb/bcftools/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bcftools)](https://hub.docker.com/r/staphb/bcftools) | <ul><li>[1.10.2](./bcftools/1.10.2/)</li><li>[1.11](./bcftools/1.11/)</li><li>[1.12](./bcftools/1.12/)</li><li>[1.13](./bcftools/1.13/)</li><li>[1.14](./bcftools/1.14/)</li><li>[1.15](./bcftools/1.15/)</li><li>[1.16](./bcftools/1.16/)</li><li>[1.17](./bcftools/1.17/)</li><li>[1.18](bcftools/1.18/)</li><li>[1.19](./bcftools/1.19/)</li><li>[1.20](./bcftools/1.20/)</li><li>[1.20.c](./bcftools/1.20.c/)</li></ul> | https://github.com/samtools/bcftools |
+| [bcftools](https://hub.docker.com/r/staphb/bcftools/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bcftools)](https://hub.docker.com/r/staphb/bcftools) | <ul><li>[1.10.2](./bcftools/1.10.2/)</li><li>[1.11](./bcftools/1.11/)</li><li>[1.12](./bcftools/1.12/)</li><li>[1.13](./bcftools/1.13/)</li><li>[1.14](./bcftools/1.14/)</li><li>[1.15](./bcftools/1.15/)</li><li>[1.16](./bcftools/1.16/)</li><li>[1.17](./bcftools/1.17/)</li><li>[1.18](bcftools/1.18/)</li><li>[1.19](./bcftools/1.19/)</li><li>[1.20](./bcftools/1.20/)</li><li>[1.20.c](./bcftools/1.20.c/)</li><li>[1.21](./bcftools/1.21/)</li></ul> | https://github.com/samtools/bcftools |
 | [bedtools](https://hub.docker.com/r/staphb/bedtools/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bedtools)](https://hub.docker.com/r/staphb/bedtools) | <ul><li>2.29.2</li><li>2.30.0</li><li>[2.31.0](bedtools/2.31.0/)</li><li>[2.31.1](bedtools/2.31.1/)</li></ul> | https://bedtools.readthedocs.io/en/latest/ <br/>https://github.com/arq5x/bedtools2 |
 | [berrywood-report-env](https://hub.docker.com/r/staphb/berrywood-report-env/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/berrywood-report-env)](https://hub.docker.com/r/staphb/berrywood-report-env) | <ul><li>1.0</li></ul> | none |
 | [blast+](https://hub.docker.com/r/staphb/blast/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/blast)](https://hub.docker.com/r/staphb/blast) | <ul><li>[2.13.0](blast/2.13.0/)</li><li>[2.14.0](blast/2.14.0/)</li><li>[2.14.1](blast/2.14.1/)</li><li>[2.15.0](blast/2.15.0/)</li><li>[2.16.0](./blast/2.16.0/)</li></ul> | https://www.ncbi.nlm.nih.gov/books/NBK279690/ |

samtools/1.21/Dockerfile

@@ -0,0 +1,100 @@
+ARG SAMTOOLS_VER="1.21"
+
+FROM ubuntu:jammy as builder
+
+ARG SAMTOOLS_VER
+
+# install dependencies required for compiling samtools
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    libncurses5-dev \
+    libbz2-dev \
+    liblzma-dev \
+    libcurl4-gnutls-dev \
+    zlib1g-dev \
+    libssl-dev \
+    libdeflate-dev \
+    gcc \
+    wget \
+    make \
+    perl \
+    bzip2 \
+    gnuplot \
+    ca-certificates
+
+# download, compile, and install samtools
+RUN wget -q https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VER}/samtools-${SAMTOOLS_VER}.tar.bz2 && \
+    tar -xjf samtools-${SAMTOOLS_VER}.tar.bz2 && \
+    cd samtools-${SAMTOOLS_VER} && \
+    ./configure && \
+    make && \
+    make install && \
+    make test
+
+### start of app stage ###
+FROM ubuntu:jammy as app
+
+ARG SAMTOOLS_VER
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="samtools"
+LABEL software.version="${SAMTOOLS_VER}"
+LABEL description="Tools (written in C using htslib) for manipulating next-generation sequencing data"
+LABEL website="https://github.com/samtools/samtools"
+LABEL license="https://github.com/samtools/samtools/blob/develop/LICENSE"
+LABEL maintainer="Shelby Bennett"
+LABEL maintainer.email="shelby.bennett@dgs.virginia.gov"
+LABEL maintainer2="Curtis Kapsak"
+LABEL maintainer2.email="kapsakcj@gmail.com"
+LABEL maintainer3="Erin Young"
+LABEL maintainer3.email="eriny@utah.gov"
+LABEL maintainer4="Kutluhan Incekara"
+LABEL maintainer4.email="kutluhan.incekara@ct.gov"
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+# install dependencies required for running samtools
+# 'gnuplot' required for plot-ampliconstats
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    perl \
+    zlib1g \
+    libncurses5 \
+    bzip2 \
+    liblzma5 \
+    libcurl3-gnutls \
+    libdeflate0 \
+    gnuplot \
+    && apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# copy in samtools executables from builder stage
+COPY --from=builder /usr/local/bin/* /usr/local/bin/
+
+ENV LC_ALL=C
+
+# final working directory is /data
+WORKDIR /data
+
+# default command is to pull up help options
+CMD ["samtools", "--help"]
+
+### start of test stage ###
+FROM app as test
+
+ARG SAMTOOLS_VER
+
+# check PATH
+RUN samtools --help
+
+# install make and wget for downloading test files
+RUN apt-get update && apt-get install --no-install-recommends -y wget ca-certificates
+
+WORKDIR /test
+
+RUN wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123.consensus.fa && \
+    wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123.primertrim.sorted.bam && \
+    wget -q https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V3/nCoV-2019.primer.bed && \
+    samtools stats SRR13957123.primertrim.sorted.bam && \
+    samtools faidx SRR13957123.consensus.fa && \
+    samtools ampliconstats nCoV-2019.primer.bed SRR13957123.primertrim.sorted.bam > SRR13957123_ampliconstats.txt && \
+    plot-ampliconstats plot SRR13957123_ampliconstats.txt && \
+    ls

samtools/1.21/README.md

@@ -0,0 +1,30 @@
+# samtools container
+
+Main tool: [samtools](https://www.htslib.org/)
+
+Code repository: https://github.com/samtools/samtools
+
+Additional tools:
+
+* perl 5.34.0
+
+Basic information on how to use this tool:
+- executable: samtools
+- help: --help
+- version: --version
+- description: Utilities for the Sequence Alignment/Map (SAM) format
+
+Additional information:
+
+This container includes samtools v1.20 compiled with **libdeflate** for a better cloud performance.
+
+Full documentation: https://www.htslib.org/doc/samtools.html
+
+## Example Usage
+
+```bash
+samtools ampliconclip -b bed.file input.bam
+
+samtools sort -T /tmp/aln.sorted -o aln.sorted.bam aln.bam
+```
+