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| Original file line number | Diff line number | Diff line change |
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| FROM ubuntu:18.04 | ||
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| # Install required packages | ||
| RUN apt-get update | ||
| RUN apt-get install -y build-essential wget git autoconf | ||
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| # Install dependencies for AUGUSTUS | ||
| RUN apt-get install -y libboost-iostreams-dev zlib1g-dev | ||
| RUN apt-get install -y libgsl-dev libboost-graph-dev libsuitesparse-dev liblpsolve55-dev libsqlite3-dev libmysql++-dev | ||
| RUN apt-get install -y libbamtools-dev | ||
| RUN apt-get install -y libboost-all-dev | ||
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| # Install additional dependencies for htslib and samtools | ||
| RUN apt-get install -y libbz2-dev liblzma-dev | ||
| RUN apt-get install -y libncurses5-dev | ||
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| # Install additional dependencies for bam2wig | ||
| RUN apt-get install -y libssl-dev libcurl3-dev | ||
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| # Build bam2wig dependencies (htslib, bfctools, samtools) | ||
| RUN git clone https://github.com/samtools/htslib.git /root/htslib | ||
| WORKDIR "/root/htslib" | ||
| RUN autoheader | ||
| RUN autoconf | ||
| RUN ./configure | ||
| RUN make | ||
| RUN make install | ||
| RUN git clone https://github.com/samtools/bcftools.git /root/bcftools | ||
| WORKDIR "/root/bcftools" | ||
| RUN autoheader | ||
| RUN autoconf | ||
| RUN ./configure | ||
| RUN make | ||
| RUN make install | ||
| RUN git clone https://github.com/samtools/samtools.git /root/samtools | ||
| WORKDIR "/root/samtools" | ||
| RUN autoheader | ||
| RUN autoconf -Wno-syntax | ||
| RUN ./configure | ||
| RUN make | ||
| RUN make install | ||
| ENV TOOLDIR="/root" | ||
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| # Clone AUGUSTUS repository | ||
| ADD / /root/augustus | ||
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| WORKDIR "/root/augustus" | ||
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| RUN sed -i "s/# COMPGENEPRED = true/COMPGENEPRED = true/g" /root/augustus/common.mk | ||
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| # Build bam2wig | ||
| RUN mkdir -p /root/augustus/bin | ||
| WORKDIR "/root/augustus/auxprogs/bam2wig" | ||
| RUN make | ||
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| # Build AUGUSTUS | ||
| WORKDIR "/root/augustus" | ||
| RUN make | ||
| RUN make install | ||
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| # Test AUGUSTUS | ||
| RUN make test | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,64 @@ | ||
| M ubuntu:18.04 | ||
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||
|
|
||
| # Install required packages | ||
| RUN apt-get update | ||
| RUN apt-get install -y build-essential wget git autoconf | ||
|
|
||
| # Install dependencies for AUGUSTUS | ||
| RUN apt-get install -y libboost-iostreams-dev zlib1g-dev | ||
| RUN apt-get install -y libgsl-dev libboost-graph-dev libsuitesparse-dev liblpsolve55-dev libsqlite3-dev libmysql++-dev | ||
| RUN apt-get install -y libbamtools-dev | ||
| RUN apt-get install -y libboost-all-dev | ||
|
|
||
| # Install additional dependencies for htslib and samtools | ||
| RUN apt-get install -y libbz2-dev liblzma-dev | ||
| RUN apt-get install -y libncurses5-dev | ||
|
|
||
| # Install additional dependencies for bam2wig | ||
| RUN apt-get install -y libssl-dev libcurl3-dev | ||
|
|
||
| # Build bam2wig dependencies (htslib, bfctools, samtools) | ||
| RUN git clone https://github.com/samtools/htslib.git /root/htslib | ||
| WORKDIR "/root/htslib" | ||
| RUN autoheader | ||
| RUN autoconf | ||
| RUN ./configure | ||
| RUN make | ||
| RUN make install | ||
| RUN git clone https://github.com/samtools/bcftools.git /root/bcftools | ||
| WORKDIR "/root/bcftools" | ||
| RUN autoheader | ||
| RUN autoconf | ||
| RUN ./configure | ||
| RUN make | ||
| RUN make install | ||
| RUN git clone https://github.com/samtools/samtools.git /root/samtools | ||
| WORKDIR "/root/samtools" | ||
| RUN autoheader | ||
| RUN autoconf -Wno-syntax | ||
| RUN ./configure | ||
| RUN make | ||
| RUN make install | ||
| ENV TOOLDIR="/root" | ||
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| # Clone AUGUSTUS repository | ||
| ADD / /root/augustus | ||
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| RUN sed -i "s/#.*MYSQL = true/MYSQL = true/g" /root/augustus/common.mk | ||
| RUN sed -i "s/# COMPGENEPRED = true/COMPGENEPRED = true/g" /root/augustus/common.mk | ||
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| # Build bam2wig | ||
| RUN mkdir -p /root/augustus/bin | ||
| WORKDIR "/root/augustus/auxprogs/bam2wig" | ||
| RUN make | ||
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| # Build AUGUSTUS | ||
| WORKDIR "/root/augustus" | ||
| RUN make | ||
| RUN make install | ||
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| # Test AUGUSTUS | ||
| RUN make test | ||
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This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,62 @@ | ||
| FROM ubuntu:18.04 | ||
|
|
||
| # Install required packages | ||
| RUN apt-get update | ||
| RUN apt-get install -y build-essential wget git autoconf | ||
|
|
||
| # Install dependencies for AUGUSTUS | ||
| RUN apt-get install -y libboost-iostreams-dev zlib1g-dev | ||
| RUN apt-get install -y libgsl-dev libboost-graph-dev libsuitesparse-dev liblpsolve55-dev libsqlite3-dev libmysql++-dev | ||
| RUN apt-get install -y libbamtools-dev | ||
| RUN apt-get install -y libboost-all-dev | ||
|
|
||
| # Install additional dependencies for htslib and samtools | ||
| RUN apt-get install -y libbz2-dev liblzma-dev | ||
| RUN apt-get install -y libncurses5-dev | ||
|
|
||
| # Install additional dependencies for bam2wig | ||
| RUN apt-get install -y libssl-dev libcurl3-dev | ||
|
|
||
| # Build bam2wig dependencies (htslib, bfctools, samtools) | ||
| RUN git clone https://github.com/samtools/htslib.git /root/htslib | ||
| WORKDIR "/root/htslib" | ||
| RUN autoheader | ||
| RUN autoconf | ||
| RUN ./configure | ||
| RUN make | ||
| RUN make install | ||
| RUN git clone https://github.com/samtools/bcftools.git /root/bcftools | ||
| WORKDIR "/root/bcftools" | ||
| RUN autoheader | ||
| RUN autoconf | ||
| RUN ./configure | ||
| RUN make | ||
| RUN make install | ||
| RUN git clone https://github.com/samtools/samtools.git /root/samtools | ||
| WORKDIR "/root/samtools" | ||
| RUN autoheader | ||
| RUN autoconf -Wno-syntax | ||
| RUN ./configure | ||
| RUN make | ||
| RUN make install | ||
| ENV TOOLDIR="/root" | ||
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| # Clone AUGUSTUS repository | ||
| ADD / /root/augustus | ||
|
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| RUN sed -i "s/# SQLITE = true/SQLITE = true/g" /root/augustus/common.mk | ||
| RUN sed -i "s/# COMPGENEPRED = true/COMPGENEPRED = true/g" /root/augustus/common.mk | ||
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| # Build bam2wig | ||
| RUN mkdir -p /root/augustus/bin | ||
| WORKDIR "/root/augustus/auxprogs/bam2wig" | ||
| RUN make | ||
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| # Build AUGUSTUS | ||
| WORKDIR "/root/augustus" | ||
| RUN make | ||
| RUN make install | ||
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| # Test AUGUSTUS | ||
| RUN make test | ||
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