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Update/svaba #1046

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8a95f25
update svaba container
Jul 11, 2024
7176341
update svaba container with LABEL and add updated tag to config
Jul 19, 2024
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2 changes: 1 addition & 1 deletion conf/containers.config
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Original file line number Diff line number Diff line change
Expand Up @@ -85,7 +85,7 @@
container = "cmopipeline/strelka2-manta-bcftools-vt:2.0.1"
}
withName: '.*RunSvABA' {
container = "cmopipeline/svaba:0.0.1"
container = "cmopipeline/svaba:0.0.2"
}
withName: 'runBRASS.*' {
container = "cmopipeline/brass:0.0.2"
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86 changes: 52 additions & 34 deletions containers/svaba/Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,38 +1,56 @@
# adapted from https://bitbucket.org/weischenfeldt/svaba/src/master/Dockerfile
# they use SvABA version 134 (4a0606eba1bfd43c3d38433b27ac7f5e4887bc1e) but that is outdated at this point so start with latest commit
FROM centos:7.3.1611
# Start with an Ubuntu image
FROM ubuntu:20.04

LABEL maintainer="Anne Marie Noronha (noronhaa@mskcc.org)" \
version.image="0.0.1"
version.image="0.0.2"

RUN yum install -y epel-release
RUN yum install -y \
git \
zlib-devel \
gcc gcc-c++ \
gcc-gfortran \
# Avoid prompts with tzdata (timezones)
ENV DEBIAN_FRONTEND=noninteractive

# Install dependencies for htslib and svaba
RUN apt update && apt install -y \
autoconf \
automake \
make \
wget \
bzip2-devel.x86_64 \
xz-devel \
bcftools

# original commit for pcawg
ENV SVABA_COMMIT 4a0606eba1bfd43c3d38433b27ac7f5e4887bc1e
# latest release commit
#ENV SVABA_COMMIT d12cf224f7a488b913eabbcf54a215e17238032c

# SvABA Version: 1.1.3 (4d7b57);
# Submodule path 'SeqLib': checked out 'f7a89a127409a3f52fdf725fa74e5438c68e48fb'
# Submodule path 'SeqLib/bwa': checked out 'c02766e3c34ac3f4af9842e20a54b7f9f4b36d0b'
# Submodule path 'SeqLib/fermi-lite': checked out '5bc90f8d70e2b66184eccbd223a3be714c914365'
# Submodule path 'SeqLib/htslib': checked out '49fdfbda20acbd73303df3c7fef84f2d972c5f8d'
RUN git clone https://github.com/walaj/svaba && \
cd svaba && \
git checkout ${SVABA_COMMIT} && \
git submodule update --init --recursive && \
./configure && \
make && \
make install

ENV PATH=/svaba/bin/:$PATH
gcc \
g++ \
git \
perl \
zlib1g-dev \
libbz2-dev \
liblzma-dev \
libcurl4-gnutls-dev \
libssl-dev \
cmake \
bcftools \
&& rm -rf /var/lib/apt/lists/*

# Clone and install htslib
WORKDIR /opt
RUN git clone --recursive https://github.com/samtools/htslib.git && \
cd htslib && \
autoheader && \
autoconf && \
./configure && \
make && \
make install

# Ensure shared libraries are noticed
RUN ldconfig

# Clone svaba
ENV SVABA_COMMIT ab39e3f656ccf34a985c4ac632426bb4be744e15
WORKDIR /opt
RUN git clone --recursive https://github.com/walaj/svaba.git && cd svaba && mkdir build && \
git checkout ${SVABA_COMMIT} && \
git submodule update --init --recursive

# Compile svaba with htslib
WORKDIR /opt/svaba/build
RUN cmake .. \
-DHTSLIB_DIR=/usr/local && \
make

# Default command can be your application run command or just an interactive shell for testing
ENV PATH "$PATH:/opt/svaba/build"