diff --git a/README.md b/README.md index 0343a92e2..79f81eb85 100644 --- a/README.md +++ b/README.md @@ -156,7 +156,7 @@ To learn more about the docker pull rate limits and the open source software pro | [FastTree](https://hub.docker.com/r/staphb/fasttree)
[![docker pulls](https://badgen.net/docker/pulls/staphb/fasttree)](https://hub.docker.com/r/staphb/fasttree) | | http://www.microbesonline.org/fasttree/ | | [FastQC](https://hub.docker.com/r/staphb/fastqc)
[![docker pulls](https://badgen.net/docker/pulls/staphb/fastqc)](https://hub.docker.com/r/staphb/fastqc) | | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
https://github.com/s-andrews/FastQC | | [fastq-scan](https://hub.docker.com/r/staphb/fastq-scan)
[![docker pulls](https://badgen.net/docker/pulls/staphb/fastq-scan)](https://hub.docker.com/r/staphb/fastq-scan) | | https://github.com/rpetit3/fastq-scan | -| [Freebayes](https://hub.docker.com/r/staphb/freebayes)
[![docker pulls](https://badgen.net/docker/pulls/staphb/freebayes)](https://hub.docker.com/r/staphb/freebayes) | | https://github.com/freebayes/freebayes | +| [Freebayes](https://hub.docker.com/r/staphb/freebayes)
[![docker pulls](https://badgen.net/docker/pulls/staphb/freebayes)](https://hub.docker.com/r/staphb/freebayes) | | https://github.com/freebayes/freebayes | | [Filtlong](https://hub.docker.com/r/staphb/filtlong)
[![docker pulls](https://badgen.net/docker/pulls/staphb/filtlong)](https://hub.docker.com/r/staphb/filtlong) | | https://github.com/rrwick/filtlong | | [FLASH](https://hub.docker.com/r/staphb/flash)
[![docker pulls](https://badgen.net/docker/pulls/staphb/flash)](https://hub.docker.com/r/staphb/flash) | | http://ccb.jhu.edu/software/FLASH | | [Flye](https://hub.docker.com/r/staphb/flye)
[![docker pulls](https://badgen.net/docker/pulls/staphb/flye)](https://hub.docker.com/r/staphb/flye) | | https://github.com/fenderglass/Flye | diff --git a/freebayes/1.3.8/Dockerfile b/freebayes/1.3.8/Dockerfile new file mode 100644 index 000000000..640220f11 --- /dev/null +++ b/freebayes/1.3.8/Dockerfile @@ -0,0 +1,89 @@ +FROM ubuntu:jammy as builder + +ARG FREEBAYES_VER="1.3.8" + +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="kitty.chase@dhhs.nc.gov" +LABEL maintainer2="Jill Hagey" +LABEL maintainer2.email="jvhagey@gmail.com" + +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 \ + libwfa2 && \ + 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 diff --git a/freebayes/1.3.8/README.md b/freebayes/1.3.8/README.md new file mode 100644 index 000000000..64d0522c9 --- /dev/null +++ b/freebayes/1.3.8/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.