adding freebayes version 1.3.8 attempt 2

freebayes/1.3.8/Dockerfile

@@ -0,0 +1,51 @@
+FROM mambaorg/micromamba:1.5.8 AS app
+
+ARG FREEBAYES_VER="1.3.7"
+
+USER root
+WORKDIR /
+
+LABEL base.image="mambaorg/micromamba:1.5.8"
+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"
+
+# 'RUN' executes code during the build
+# Install dependencies via apt-get or yum if using a centos or fedora base
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates \
+    procps && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN micromamba install --name base -c conda-forge -c bioconda -c defaults freebayes=${FREEBAYES_VER} && \
+    micromamba clean -a -f -y && \
+    mkdir /data
+
+ENV PATH="/opt/conda/bin/:${PATH}" \
+    LC_ALL=C.UTF-8
+
+# 'CMD' instructions set a default command when the container is run. This is typically 'tool --help.'
+CMD [ "freebayes", "--help" ]
+
+# set final working directory to /data
+WORKDIR /data
+
+FROM app AS test
+
+# set working directory so that all test inputs & outputs are kept in /test
+WORKDIR /test
+
+RUN freebayes --help
+
+RUN wget https://github.com/StaPH-B/docker-builds/raw/master/tests/SARS-CoV-2/SRR13957123.sorted.bam && \
+    wget https://raw.githubusercontent.com/artic-network/primer-schemes/refs/heads/master/nCoV-2019/V5.3.2/SARS-CoV-2.reference.fasta && \
+    freebayes -f SARS-CoV-2.reference.fasta SRR13957123.sorted.bam > var.vcf && \
+    head var.vcf

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.