diff --git a/README.md b/README.md index 2a031db91..584bf2ff7 100644 --- a/README.md +++ b/README.md @@ -177,7 +177,7 @@ To learn more about the docker pull rate limits and the open source software pro | [heatcluster](https://hub.docker.com/r/staphb/heatcluster)
[![docker pulls](https://badgen.net/docker/pulls/staphb/heatcluster)](https://hub.docker.com/r/staphb/heatcluster) | | https://github.com/DrB-S/heatcluster/tree/main | | [hmmer](https://hub.docker.com/r/staphb/hmmer)
[![docker pulls](https://badgen.net/docker/pulls/staphb/hmmer)](https://hub.docker.com/r/staphb/hmmer) | | http://hmmer.org/ | | [homopolish](https://hub.docker.com/r/staphb/homopolish)
[![docker pulls](https://badgen.net/docker/pulls/staphb/homopolish)](https://hub.docker.com/r/staphb/homopolish) | | https://github.com/ythuang0522/homopolish/ | -| [htslib](https://hub.docker.com/r/staphb/htslib)
[![docker pulls](https://badgen.net/docker/pulls/staphb/htslib)](https://hub.docker.com/r/staphb/htslib) | | https://www.htslib.org/ | +| [htslib](https://hub.docker.com/r/staphb/htslib)
[![docker pulls](https://badgen.net/docker/pulls/staphb/htslib)](https://hub.docker.com/r/staphb/htslib) | | https://www.htslib.org/ | | [iqtree](https://hub.docker.com/r/staphb/iqtree/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree)](https://hub.docker.com/r/staphb/iqtree) | | http://www.iqtree.org/ | | [iqtree2](https://hub.docker.com/r/staphb/iqtree2/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree2)](https://hub.docker.com/r/staphb/iqtree2) | | http://www.iqtree.org/ | | [IPA](https://hub.docker.com/r/staphb/pbipa)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pbipa)](https://hub.docker.com/r/staphb/pbipa) | | https://github.com/PacificBiosciences/pbipa | diff --git a/htslib/1.21/Dockerfile b/htslib/1.21/Dockerfile new file mode 100644 index 000000000..47f42bfc8 --- /dev/null +++ b/htslib/1.21/Dockerfile @@ -0,0 +1,97 @@ +# for easy upgrade later. ARG variables only persist during build time +ARG HTSLIB_VER="1.21" + +FROM ubuntu:jammy as builder + +ARG HTSLIB_VER + +# install dependencies, cleanup apt garbage +# It's helpful when they're all listed on https://github.com/samtools/htslib/blob/develop/INSTALL +RUN apt-get update && apt-get install --no-install-recommends -y \ + wget \ + ca-certificates \ + make \ + bzip2 \ + autoconf \ + automake \ + make \ + gcc \ + perl \ + zlib1g-dev \ + libbz2-dev \ + liblzma-dev \ + libcurl4-gnutls-dev \ + libssl-dev \ + libdeflate-dev \ + procps && \ + rm -rf /var/lib/apt/lists/* && apt-get autoclean + +# get htslib, compile, install, run test suite +RUN wget -q https://github.com/samtools/htslib/releases/download/${HTSLIB_VER}/htslib-${HTSLIB_VER}.tar.bz2 && \ + tar -vxjf htslib-${HTSLIB_VER}.tar.bz2 && \ + rm -v htslib-${HTSLIB_VER}.tar.bz2 && \ + cd htslib-${HTSLIB_VER} && \ + ./configure && \ + make && \ + make install && \ + make test + +### start of app stage ### +FROM ubuntu:jammy as app + +ARG HTSLIB_VER + +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="htslib" +LABEL software.version="${HTSLIB_VER}" +LABEL description="A C library for reading/writing high-throughput sequencing data" +LABEL website="https://github.com/samtools/htslib" +LABEL license="https://github.com/samtools/htslib/blob/develop/LICENSE" +LABEL maintainer="Erin Young" +LABEL maintainer.email="eriny@utah.gov" +LABEL maintainer2="Curtis Kapsak" +LABEL maintainer2.email="kapsakcj@gmail.com" + +# install runtime dependencies & cleanup apt garbage +# installed as recommend here: https://github.com/samtools/htslib/blob/develop/INSTALL#L31 +RUN apt-get update && apt-get install --no-install-recommends -y \ + bzip2 \ + zlib1g \ + libbz2-1.0 \ + liblzma5 \ + libcurl3-gnutls \ + libdeflate0 \ + ca-certificates \ + && apt-get autoclean && rm -rf /var/lib/apt/lists/* + +# copy in htslib executables from builder stage +COPY --from=builder /usr/local/bin/* /usr/local/bin/ +COPY --from=builder /usr/local/lib/ /usr/local/lib/ +COPY --from=builder /usr/local/include/ /usr/local/include/ + +# set locale settings for singularity compatibility +ENV LC_ALL=C + +# set working directory +WORKDIR /data + +# default command is to show help options +CMD ["htsfile", "--help"] + +### start of test stage ### +FROM app as test + +# check that these three executables are available +RUN bgzip --help && tabix --help && htsfile --help + +RUN apt-get update && apt-get install --no-install-recommends -y wget + +# use on actual files +RUN wget -q https://github.com/StaPH-B/docker-builds/raw/master/tests/SARS-CoV-2/SRR13957123_1.fastq.gz && \ + gunzip SRR13957123_1.fastq.gz && \ + bgzip SRR13957123_1.fastq + +# FYI Test suite "make test" now performed in the builder stage since app and +# test stages do not include htslib source code. +# This is to avoid having to re-download source code simply to run test suite \ No newline at end of file diff --git a/htslib/1.21/README.md b/htslib/1.21/README.md new file mode 100644 index 000000000..1b505f02c --- /dev/null +++ b/htslib/1.21/README.md @@ -0,0 +1,35 @@ +# htslib container + +Main tool: [htslib](https://www.htslib.org/) + +Code repository: https://github.com/samtools/htslib + +Additional tools: + +* perl 5.34.0 + +Basic information on how to use this tool: +- executable: htsfile +- help: --help +- version: --version +- description: The htsfile utility attempts to identify what kind of high-throughput sequencing data files the specified files are, and provides minimal viewing capabilities for some kinds of data file. + +Additional information: + +This container includes htslib v1.21 compiled with **libdeflate** for a better cloud performance. + +Full documentation: https://www.htslib.org/doc/samtools.html + +## Example Usage + +```bash +# determine file formats for various BAM and SAM files +$ htsfile tests/SARS-CoV-2/SRR13957123.primertrim.sorted.bam +tests/SARS-CoV-2/SRR13957123.primertrim.sorted.bam: BAM version 1 compressed sequence data + +$ htsfile ce_tag_padded.sam +ce_tag_padded.sam: SAM version 1.4 sequence text + +# compresses sample.fastq to sample.fastq.gz in BGZF format (blocked GNU Zip Format) +$ bgzip sample.fastq +```