update freebayes1.3.7

README.md

@@ -143,7 +143,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [FastTree](https://hub.docker.com/r/staphb/fasttree) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/fasttree)](https://hub.docker.com/r/staphb/fasttree) | <ul><li>2.1.11</li></ul> | http://www.microbesonline.org/fasttree/ |
 | [FastQC](https://hub.docker.com/r/staphb/fastqc) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/fastqc)](https://hub.docker.com/r/staphb/fastqc) | <ul><li>0.11.8</li><li>0.11.9</li><li>0.12.1</li></ul> | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ <br/> https://github.com/s-andrews/FastQC |
 | [fastq-scan](https://hub.docker.com/r/staphb/fastq-scan) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/fastq-scan)](https://hub.docker.com/r/staphb/fastq-scan) | <ul><li>0.4.3</li><li>0.4.4</li><li>1.0.0</li><li>1.0.1</li></ul> | https://github.com/rpetit3/fastq-scan |
-| [Freebayes](https://hub.docker.com/r/staphb/freebayes) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/freebayes)](https://hub.docker.com/r/staphb/freebayes) | <ul><li>1.3.6</li></ul> | https://github.com/freebayes/freebayes |
+| [Freebayes](https://hub.docker.com/r/staphb/freebayes) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/freebayes)](https://hub.docker.com/r/staphb/freebayes) | <ul><li>1.3.6</li><li>1.3.7</li><li>1.3.7</li><li>1.3.7</li></ul> | https://github.com/freebayes/freebayes |
 | [Filtlong](https://hub.docker.com/r/staphb/filtlong) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/filtlong)](https://hub.docker.com/r/staphb/filtlong) | <ul><li>0.2.0</li><li>0.2.1</li></ul> | https://github.com/rrwick/filtlong |
 | [FLASH](https://hub.docker.com/r/staphb/flash) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/flash)](https://hub.docker.com/r/staphb/flash) | <ul><li>1.2.11</li></ul> | http://ccb.jhu.edu/software/FLASH |
 | [Flye](https://hub.docker.com/r/staphb/flye) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/flye)](https://hub.docker.com/r/staphb/flye) | <ul><li>2.5</li><li>2.7</li><li>2.8</li><li>2.9</li><li>2.9.1</li><li>2.9.2</li></ul> | https://github.com/fenderglass/Flye |

freebayes/1.3.7/Dockerfile

@@ -0,0 +1,88 @@
+FROM ubuntu:jammy as builder
+
+ARG FREEBAYES_VER="1.3.7"
+
+ARG DEBIAN_FRONTEND=noninteractive
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    ca-certificates \
+    build-essential \
+    pkg-config \
+    meson \
+    cmake \
+    zlib1g-dev \
+    liblzma-dev \
+    libbz2-dev \
+    libncurses5-dev \
+    libc6 \
+    libgcc-s1 \
+    libstdc++6 \
+    libvcflib1 \
+    libvcflib-tools \
+    libseqlib-dev \
+    libvcflib-dev \
+    bc \
+    parallel \
+    ninja-build \
+    wget \
+    samtools \
+    vcftools && \
+    rm -rf /var/lib/apt/lists/* && apt-get autoclean
+
+RUN wget https://github.com/freebayes/freebayes/archive/refs/tags/v${FREEBAYES_VER}.tar.gz && \
+    tar -xvzf v${FREEBAYES_VER}.tar.gz && \
+    mv freebayes-${FREEBAYES_VER} /freebayes && \
+    cd /freebayes && \
+    meson build/ && \
+    cd build && \
+    ninja
+
+RUN /freebayes/build/freebayes --help
+
+FROM ubuntu:jammy as app
+
+LABEL base.image="ubuntu:focal"
+LABEL dockerfile.version="1"
+LABEL software="FreeBayes"
+LABEL software.version="1.3.7"
+LABEL description="FreeBayes is a haplotype-based variant detector and is a great tool for calling variants from a population."
+LABEL website="https://github.com/freebayes/freebayes"
+LABEL license="https://github.com/freebayes/freebayes/blob/master/LICENSE"
+LABEL maintainer="Kitty Chase"
+LABEL maintainer.email="[email protected]"
+LABEL maintainer2="Jill Hagey"
+LABEL maintainer2.email="[email protected]"
+
+COPY --from=builder /freebayes/build/* /usr/local/bin/
+
+# vcftools version is 0.1.16
+# samtools version is 1.13
+ARG DEBIAN_FRONTEND=noninteractive
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    bc \
+    ca-certificates \
+    libseqlib-dev \
+    libvcflib-tools \
+    parallel \
+    procps \
+    samtools \
+    vcftools \
+    wget && \
+    rm -rf /var/lib/apt/lists/* && apt-get autoclean
+
+RUN freebayes --help && vcftools --help && samtools --help
+
+ENV LC_ALL=C
+
+WORKDIR /data
+
+CMD freebayes --help
+
+# new base for testing
+FROM app as test
+
+RUN freebayes --help && vcftools --help && samtools --help
+
+RUN wget -q https://github.com/StaPH-B/docker-builds/raw/master/tests/SARS-CoV-2/SRR13957123.sorted.bam && \
+    wget -q https://raw.githubusercontent.com/UPHL-BioNGS/Cecret/master/genomes/MN908947.3.fasta && \
+    freebayes -f MN908947.3.fasta SRR13957123.sorted.bam > var.vcf && \
+    head var.vcf

freebayes/1.3.7/README.md

@@ -0,0 +1,30 @@
+# FreeBayes Container
+
+## Documentation and Overview
+
+Main Tool: FreeBayes - [Haplotype-based variant detection from short-read sequencing](https://arxiv.org/abs/1207.3907)
+
+Additional tools:
+- vcftools version is 0.1.16
+- samtools version is 1.13
+
+Full documentation: https://github.com/freebayes/freebayes 
+
+FreeBayes is a haplotype-based variant detector and is a great tool for calling variants from a population.
+
+FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.
+
+FreeBayes is haplotype-based, in the sense that it calls variants based on the literal sequences of reads aligned to a particular target, not their precise alignment. This model is a straightforward generalization of previous ones (e.g. PolyBayes, samtools, GATK) which detect or report variants based on alignments. This method avoids one of the core problems with alignment-based variant detection — that identical sequences may have multiple possible alignments:”
+
+## Usage
+
+Basic usage:
+```
+freebayes -f [REFERENCE] [OPTIONS] [BAM FILES] >[OUTPUT]
+```
+Example usage:
+```
+freebayes --bam Sample_1_sorted.bam --ploidy 1 --fasta-reference reference.fasta --vcf Sample1_freebayes.vcf
+```
+
+There are LOTS of options so use `freebayes --help` to get full list.