From 4b7d67890a1059d93d3583d32247ff6ece911399 Mon Sep 17 00:00:00 2001 From: Kitty Chase Date: Thu, 26 Oct 2023 14:19:31 -0400 Subject: [PATCH 01/11] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 316a18592..b8823add8 100644 --- a/README.md +++ b/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)
[![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 | From 6efef3405ac06ae1ae0721016b2e04bbcfee2d43 Mon Sep 17 00:00:00 2001 From: Kitty Chase Date: Thu, 26 Oct 2023 14:32:04 -0400 Subject: [PATCH 02/11] freebayes/1.3.7 --- freebayes/1.3.7 | 86 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100644 freebayes/1.3.7 diff --git a/freebayes/1.3.7 b/freebayes/1.3.7 new file mode 100644 index 000000000..99c7f82aa --- /dev/null +++ b/freebayes/1.3.7 @@ -0,0 +1,86 @@ +FROM ubuntu:focal as app + +# for easy upgrade later. ARG variables only persist during image build time +ARG FREEBAYES_VER="1.3.7" +ARG SAMTOOLSVER="1.14" +ARG VCFTOOLS_VER="0.1.16" + +# metadata +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" + +# Install dependencies +ARG DEBIAN_FRONTEND=noninteractive +RUN apt-get update && apt-get install -y --no-install-recommends \ + ca-certificates \ + build-essential \ + pkg-config \ + meson \ + zlib1g-dev \ + liblzma-dev \ + libbz2-dev \ + libncurses5-dev \ + libc6 \ + libgcc-s1 \ + libstdc++6 \ + libvcflib1 \ + libvcflib-tools \ + bc \ + parallel \ + ninja-build \ + wget && \ + rm -rf /var/lib/apt/lists/* && apt-get autoclean + +# Build and install samtools +RUN wget https://github.com/samtools/samtools/releases/download/${SAMTOOLSVER}/samtools-${SAMTOOLSVER}.tar.bz2 && \ + tar -xjf samtools-${SAMTOOLSVER}.tar.bz2 && \ + rm samtools-${SAMTOOLSVER}.tar.bz2 && \ + cd samtools-${SAMTOOLSVER} && \ + ./configure && \ + make && \ + make install + +# Build and install vcftools +RUN wget https://github.com/vcftools/vcftools/releases/download/v${VCFTOOLS_VER}/vcftools-${VCFTOOLS_VER}.tar.gz && \ + tar -vxzf vcftools-${VCFTOOLS_VER}.tar.gz && \ + rm vcftools-${VCFTOOLS_VER}.tar.gz && \ + cd vcftools-${VCFTOOLS_VER} && \ + ./configure && \ + make && \ + make install + +# Build and install freebayes +RUN wget https://github.com/freebayes/freebayes/releases/download/v${FREEBAYES_VER}/freebayes-${FREEBAYES_VER}-src.tar.gz && \ + tar -xvzf freebayes-${FREEBAYES_VER}-src.tar.gz && \ + rm freebayes-${FREEBAYES_VER}-src.tar.gz && \ + cd freebayes && \ + meson build/ --buildtype debug && \ + cd build && \ + ninja && \ + mkdir /data + +# set perl locale settings +# Required by most tools that use perl with singularity so we can use container with both docker and singularity +ENV LC_ALL=C + +# Add files paths of software +ENV PATH="${PATH}:/freebayes/build\ +:/samtools-${SAMTOOLSVER}\ +:/vcftools-${VCFTOOLS_VER}" + +# Add references and entrypoint script +WORKDIR /data + +# new base for testing +FROM app as test + +# Run test +RUN cd /freebayes/build && \ + ninja test From 6e30a0a784bf4ded7e64d30381d7cd28973e90f9 Mon Sep 17 00:00:00 2001 From: Kitty Chase Date: Thu, 26 Oct 2023 14:33:45 -0400 Subject: [PATCH 03/11] Update 1.3.7 --- freebayes/1.3.7 | 85 ------------------------------------------------- 1 file changed, 85 deletions(-) diff --git a/freebayes/1.3.7 b/freebayes/1.3.7 index 99c7f82aa..8b1378917 100644 --- a/freebayes/1.3.7 +++ b/freebayes/1.3.7 @@ -1,86 +1 @@ -FROM ubuntu:focal as app -# for easy upgrade later. ARG variables only persist during image build time -ARG FREEBAYES_VER="1.3.7" -ARG SAMTOOLSVER="1.14" -ARG VCFTOOLS_VER="0.1.16" - -# metadata -LABEL base.image="ubuntu:focal" -LABEL dockerfile.version="1" -LABEL software="FreeBayes" -LABEL software.version="1.3.7" -LABEL description="FreeBayes is a haplotype-based variant detector and is a great tool for calling variants from a population." -LABEL website="https://github.com/freebayes/freebayes" -LABEL license="https://github.com/freebayes/freebayes/blob/master/LICENSE" -LABEL maintainer="Kitty Chase" -LABEL maintainer.email="kitty.chase@dhhs.nc.gov" - -# Install dependencies -ARG DEBIAN_FRONTEND=noninteractive -RUN apt-get update && apt-get install -y --no-install-recommends \ - ca-certificates \ - build-essential \ - pkg-config \ - meson \ - zlib1g-dev \ - liblzma-dev \ - libbz2-dev \ - libncurses5-dev \ - libc6 \ - libgcc-s1 \ - libstdc++6 \ - libvcflib1 \ - libvcflib-tools \ - bc \ - parallel \ - ninja-build \ - wget && \ - rm -rf /var/lib/apt/lists/* && apt-get autoclean - -# Build and install samtools -RUN wget https://github.com/samtools/samtools/releases/download/${SAMTOOLSVER}/samtools-${SAMTOOLSVER}.tar.bz2 && \ - tar -xjf samtools-${SAMTOOLSVER}.tar.bz2 && \ - rm samtools-${SAMTOOLSVER}.tar.bz2 && \ - cd samtools-${SAMTOOLSVER} && \ - ./configure && \ - make && \ - make install - -# Build and install vcftools -RUN wget https://github.com/vcftools/vcftools/releases/download/v${VCFTOOLS_VER}/vcftools-${VCFTOOLS_VER}.tar.gz && \ - tar -vxzf vcftools-${VCFTOOLS_VER}.tar.gz && \ - rm vcftools-${VCFTOOLS_VER}.tar.gz && \ - cd vcftools-${VCFTOOLS_VER} && \ - ./configure && \ - make && \ - make install - -# Build and install freebayes -RUN wget https://github.com/freebayes/freebayes/releases/download/v${FREEBAYES_VER}/freebayes-${FREEBAYES_VER}-src.tar.gz && \ - tar -xvzf freebayes-${FREEBAYES_VER}-src.tar.gz && \ - rm freebayes-${FREEBAYES_VER}-src.tar.gz && \ - cd freebayes && \ - meson build/ --buildtype debug && \ - cd build && \ - ninja && \ - mkdir /data - -# set perl locale settings -# Required by most tools that use perl with singularity so we can use container with both docker and singularity -ENV LC_ALL=C - -# Add files paths of software -ENV PATH="${PATH}:/freebayes/build\ -:/samtools-${SAMTOOLSVER}\ -:/vcftools-${VCFTOOLS_VER}" - -# Add references and entrypoint script -WORKDIR /data - -# new base for testing -FROM app as test - -# Run test -RUN cd /freebayes/build && \ - ninja test From fc6da0d4ba8f3db1ffd9f7cb3edfda4591976151 Mon Sep 17 00:00:00 2001 From: Kitty Chase Date: Thu, 26 Oct 2023 14:37:48 -0400 Subject: [PATCH 04/11] Delete freebayes/1.3.7 --- freebayes/1.3.7 | 1 - 1 file changed, 1 deletion(-) delete mode 100644 freebayes/1.3.7 diff --git a/freebayes/1.3.7 b/freebayes/1.3.7 deleted file mode 100644 index 8b1378917..000000000 --- a/freebayes/1.3.7 +++ /dev/null @@ -1 +0,0 @@ - From 54e3e121614ac9a263fe80b3cae9f7539bbc94fb Mon Sep 17 00:00:00 2001 From: Kitty Chase Date: Thu, 26 Oct 2023 14:39:23 -0400 Subject: [PATCH 05/11] Create Dockerfile --- freebayes/1.3.7/Dockerfile | 86 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100644 freebayes/1.3.7/Dockerfile diff --git a/freebayes/1.3.7/Dockerfile b/freebayes/1.3.7/Dockerfile new file mode 100644 index 000000000..99c7f82aa --- /dev/null +++ b/freebayes/1.3.7/Dockerfile @@ -0,0 +1,86 @@ +FROM ubuntu:focal as app + +# for easy upgrade later. ARG variables only persist during image build time +ARG FREEBAYES_VER="1.3.7" +ARG SAMTOOLSVER="1.14" +ARG VCFTOOLS_VER="0.1.16" + +# metadata +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" + +# Install dependencies +ARG DEBIAN_FRONTEND=noninteractive +RUN apt-get update && apt-get install -y --no-install-recommends \ + ca-certificates \ + build-essential \ + pkg-config \ + meson \ + zlib1g-dev \ + liblzma-dev \ + libbz2-dev \ + libncurses5-dev \ + libc6 \ + libgcc-s1 \ + libstdc++6 \ + libvcflib1 \ + libvcflib-tools \ + bc \ + parallel \ + ninja-build \ + wget && \ + rm -rf /var/lib/apt/lists/* && apt-get autoclean + +# Build and install samtools +RUN wget https://github.com/samtools/samtools/releases/download/${SAMTOOLSVER}/samtools-${SAMTOOLSVER}.tar.bz2 && \ + tar -xjf samtools-${SAMTOOLSVER}.tar.bz2 && \ + rm samtools-${SAMTOOLSVER}.tar.bz2 && \ + cd samtools-${SAMTOOLSVER} && \ + ./configure && \ + make && \ + make install + +# Build and install vcftools +RUN wget https://github.com/vcftools/vcftools/releases/download/v${VCFTOOLS_VER}/vcftools-${VCFTOOLS_VER}.tar.gz && \ + tar -vxzf vcftools-${VCFTOOLS_VER}.tar.gz && \ + rm vcftools-${VCFTOOLS_VER}.tar.gz && \ + cd vcftools-${VCFTOOLS_VER} && \ + ./configure && \ + make && \ + make install + +# Build and install freebayes +RUN wget https://github.com/freebayes/freebayes/releases/download/v${FREEBAYES_VER}/freebayes-${FREEBAYES_VER}-src.tar.gz && \ + tar -xvzf freebayes-${FREEBAYES_VER}-src.tar.gz && \ + rm freebayes-${FREEBAYES_VER}-src.tar.gz && \ + cd freebayes && \ + meson build/ --buildtype debug && \ + cd build && \ + ninja && \ + mkdir /data + +# set perl locale settings +# Required by most tools that use perl with singularity so we can use container with both docker and singularity +ENV LC_ALL=C + +# Add files paths of software +ENV PATH="${PATH}:/freebayes/build\ +:/samtools-${SAMTOOLSVER}\ +:/vcftools-${VCFTOOLS_VER}" + +# Add references and entrypoint script +WORKDIR /data + +# new base for testing +FROM app as test + +# Run test +RUN cd /freebayes/build && \ + ninja test From 1696cf1302817c7250e2de0a317b783dbca1ec92 Mon Sep 17 00:00:00 2001 From: Kitty Chase Date: Thu, 26 Oct 2023 14:40:04 -0400 Subject: [PATCH 06/11] Create README.md --- freebayes/1.3.7/README.md | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 freebayes/1.3.7/README.md diff --git a/freebayes/1.3.7/README.md b/freebayes/1.3.7/README.md new file mode 100644 index 000000000..0f9b03646 --- /dev/null +++ b/freebayes/1.3.7/README.md @@ -0,0 +1,26 @@ +# FreeBayes Container + +## Documentation and Overview + +Main Tool: FreeBayes - [Haplotype-based variant detection from short-read sequencing](https://arxiv.org/abs/1207.3907) + +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. From 2e20059266c89c0d4bad217f83586e8574bc915b Mon Sep 17 00:00:00 2001 From: Kitty Chase Date: Thu, 26 Oct 2023 14:42:43 -0400 Subject: [PATCH 07/11] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index b8823add8..768dbd3d7 100644 --- a/README.md +++ b/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)
[![docker pulls](https://badgen.net/docker/pulls/staphb/fasttree)](https://hub.docker.com/r/staphb/fasttree) |
  • 2.1.11
| 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) |
  • 0.11.8
  • 0.11.9
  • 0.12.1
| 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) |
  • 0.4.3
  • 0.4.4
  • 1.0.0
  • 1.0.1
| 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) |
  • 1.3.6
  • 1.3.7
| 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) |
  • 1.3.6
  • 1.3.7
  • 1.3.7
  • 1.3.7
| 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) |
  • 0.2.0
  • 0.2.1
| 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) |
  • 1.2.11
| 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) |
  • 2.5
  • 2.7
  • 2.8
  • 2.9
  • 2.9.1
  • 2.9.2
| https://github.com/fenderglass/Flye | From 76aa54c66bc2b0234840c053b391558a6384b45e Mon Sep 17 00:00:00 2001 From: Kitty Chase Date: Fri, 27 Oct 2023 08:57:26 -0400 Subject: [PATCH 08/11] Update Dockerfile --- freebayes/1.3.7/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/freebayes/1.3.7/Dockerfile b/freebayes/1.3.7/Dockerfile index 99c7f82aa..205e7ed0e 100644 --- a/freebayes/1.3.7/Dockerfile +++ b/freebayes/1.3.7/Dockerfile @@ -57,7 +57,7 @@ RUN wget https://github.com/vcftools/vcftools/releases/download/v${VCFTOOLS_VER} make install # Build and install freebayes -RUN wget https://github.com/freebayes/freebayes/releases/download/v${FREEBAYES_VER}/freebayes-${FREEBAYES_VER}-src.tar.gz && \ +RUN wget https://github.com/freebayes/freebayes/archive/refs/tags/v${FREEBAYES_VER}.tar.gz && \ tar -xvzf freebayes-${FREEBAYES_VER}-src.tar.gz && \ rm freebayes-${FREEBAYES_VER}-src.tar.gz && \ cd freebayes && \ From abac1f6cf833369d8cfa35077dca14557550bc8d Mon Sep 17 00:00:00 2001 From: Young Date: Fri, 27 Oct 2023 09:44:04 -0600 Subject: [PATCH 09/11] Changed freebayes path --- freebayes/1.3.7/Dockerfile | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/freebayes/1.3.7/Dockerfile b/freebayes/1.3.7/Dockerfile index 205e7ed0e..73dadca42 100644 --- a/freebayes/1.3.7/Dockerfile +++ b/freebayes/1.3.7/Dockerfile @@ -58,9 +58,9 @@ RUN wget https://github.com/vcftools/vcftools/releases/download/v${VCFTOOLS_VER} # Build and install freebayes RUN wget https://github.com/freebayes/freebayes/archive/refs/tags/v${FREEBAYES_VER}.tar.gz && \ - tar -xvzf freebayes-${FREEBAYES_VER}-src.tar.gz && \ - rm freebayes-${FREEBAYES_VER}-src.tar.gz && \ - cd freebayes && \ + tar -xvzf v${FREEBAYES_VER}.tar.gz && \ + rm v${FREEBAYES_VER}.tar.gz && \ + cd freebayes-v${FREEBAYES_VER} && \ meson build/ --buildtype debug && \ cd build && \ ninja && \ @@ -71,7 +71,7 @@ RUN wget https://github.com/freebayes/freebayes/archive/refs/tags/v${FREEBAYES_V ENV LC_ALL=C # Add files paths of software -ENV PATH="${PATH}:/freebayes/build\ +ENV PATH="${PATH}:/freebayes-v${FREEBAYES_VER}/build\ :/samtools-${SAMTOOLSVER}\ :/vcftools-${VCFTOOLS_VER}" From fe4da9e6b9227801d7060500cf1394f70468a765 Mon Sep 17 00:00:00 2001 From: Young Date: Fri, 27 Oct 2023 12:00:36 -0600 Subject: [PATCH 10/11] remove ninja tests --- freebayes/1.3.7/Dockerfile | 126 +++++++++++++++++++------------------ 1 file changed, 64 insertions(+), 62 deletions(-) diff --git a/freebayes/1.3.7/Dockerfile b/freebayes/1.3.7/Dockerfile index 73dadca42..d2eae7c15 100644 --- a/freebayes/1.3.7/Dockerfile +++ b/freebayes/1.3.7/Dockerfile @@ -1,11 +1,45 @@ -FROM ubuntu:focal as app +FROM ubuntu:jammy as builder -# for easy upgrade later. ARG variables only persist during image build time ARG FREEBAYES_VER="1.3.7" -ARG SAMTOOLSVER="1.14" -ARG VCFTOOLS_VER="0.1.16" -# metadata +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-${FREEBAYES_VER} /freebayes && \ + cd /freebayes && \ + meson build/ && \ + cd build && \ + ninja + +RUN /freebayes/build/freebayes --help + +FROM ubuntu:jammy as app + LABEL base.image="ubuntu:focal" LABEL dockerfile.version="1" LABEL software="FreeBayes" @@ -15,72 +49,40 @@ LABEL website="https://github.com/freebayes/freebayes" LABEL license="https://github.com/freebayes/freebayes/blob/master/LICENSE" LABEL maintainer="Kitty Chase" LABEL maintainer.email="kitty.chase@dhhs.nc.gov" +LABEL maintainer2="Jill Hagey" +LABEL maintainer2.email="jvhagey@gmail.com" -# Install dependencies +COPY --from=builder /freebayes/build/* /usr/local/bin/ + +# vcftools version is 0.1.16 +# samtools version is 1.13 ARG DEBIAN_FRONTEND=noninteractive RUN apt-get update && apt-get install -y --no-install-recommends \ - ca-certificates \ - build-essential \ - pkg-config \ - meson \ - zlib1g-dev \ - liblzma-dev \ - libbz2-dev \ - libncurses5-dev \ - libc6 \ - libgcc-s1 \ - libstdc++6 \ - libvcflib1 \ - libvcflib-tools \ - bc \ - parallel \ - ninja-build \ - wget && \ - rm -rf /var/lib/apt/lists/* && apt-get autoclean - -# Build and install samtools -RUN wget https://github.com/samtools/samtools/releases/download/${SAMTOOLSVER}/samtools-${SAMTOOLSVER}.tar.bz2 && \ - tar -xjf samtools-${SAMTOOLSVER}.tar.bz2 && \ - rm samtools-${SAMTOOLSVER}.tar.bz2 && \ - cd samtools-${SAMTOOLSVER} && \ - ./configure && \ - make && \ - make install - -# Build and install vcftools -RUN wget https://github.com/vcftools/vcftools/releases/download/v${VCFTOOLS_VER}/vcftools-${VCFTOOLS_VER}.tar.gz && \ - tar -vxzf vcftools-${VCFTOOLS_VER}.tar.gz && \ - rm vcftools-${VCFTOOLS_VER}.tar.gz && \ - cd vcftools-${VCFTOOLS_VER} && \ - ./configure && \ - make && \ - make install + bc \ + ca-certificates \ + libseqlib-dev \ + libvcflib-tools \ + parallel \ + procps \ + samtools \ + vcftools \ + wget && \ + rm -rf /var/lib/apt/lists/* && apt-get autoclean -# Build and install freebayes -RUN wget https://github.com/freebayes/freebayes/archive/refs/tags/v${FREEBAYES_VER}.tar.gz && \ - tar -xvzf v${FREEBAYES_VER}.tar.gz && \ - rm v${FREEBAYES_VER}.tar.gz && \ - cd freebayes-v${FREEBAYES_VER} && \ - meson build/ --buildtype debug && \ - cd build && \ - ninja && \ - mkdir /data +RUN freebayes --help && vcftools --help && samtools --help -# set perl locale settings -# Required by most tools that use perl with singularity so we can use container with both docker and singularity ENV LC_ALL=C -# Add files paths of software -ENV PATH="${PATH}:/freebayes-v${FREEBAYES_VER}/build\ -:/samtools-${SAMTOOLSVER}\ -:/vcftools-${VCFTOOLS_VER}" - -# Add references and entrypoint script WORKDIR /data +CMD freebayes --help + # new base for testing FROM app as test -# Run test -RUN cd /freebayes/build && \ - ninja 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 From 23c6c908c92809c12bab2b850cc319de81559f05 Mon Sep 17 00:00:00 2001 From: Young Date: Fri, 27 Oct 2023 12:26:44 -0600 Subject: [PATCH 11/11] Update README.md to include vcftools and samtools --- freebayes/1.3.7/README.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/freebayes/1.3.7/README.md b/freebayes/1.3.7/README.md index 0f9b03646..64d0522c9 100644 --- a/freebayes/1.3.7/README.md +++ b/freebayes/1.3.7/README.md @@ -4,6 +4,10 @@ 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.