dockerfile

[sybrohee]

I don't know if it is of interest for anyone but I could not compile BamHash easily, at least using the makefile... but after a bit of struggling, I could have it working. This is a dockerfile I share (so this post is not an issue)

Remarks I advise to use ubuntu 16.04 because newer version raise a lot of warnings (but it seems to be working) I don't use the provided makefile at it seems that the arguments may be not placed in the right order preventing the compilation

FROM ubuntu:16.04
RUN apt update
RUN     apt-get install -y \
        build-essential \
        unzip \
        libssl-dev \
        zlib1g-dev \
        libbz2-dev \
        git \
        liblzma-dev \
        wget


WORKDIR /
RUN wget https://github.com/samtools/htslib/archive/refs/tags/1.9.zip -O htslib_1.9.zip
RUN unzip htslib_1.9.zip
WORKDIR htslib-1.9
RUN make
RUN make install
WORKDIR /

RUN git clone https://github.com/DecodeGenetics/BamHash.git
RUN mv BamHash  BamHash-1.2
WORKDIR BamHash-1.2
RUN git reset --hard b64352c



RUN g++ -std=c++11 -pthread -I. -Wno-deprecated-declarations -I/usr/local//include -O3 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=0 -DSEQAN_HAS_ZLIB=1 -c bamhash_checksum_common.cpp -o bamhash_checksum_common.o
RUN g++ -std=c++11 -pthread -I. -Wno-deprecated-declarations -I/usr/local//include -O3 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=0 -DSEQAN_HAS_ZLIB=1 -c bamhash_checksum_bam.cpp -o bamhash_checksum_bam.o
RUN g++ -std=c++11 -pthread -I. -Wno-deprecated-declarations -I/usr/local//include -O3 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=0 -DSEQAN_HAS_ZLIB=1 -c bamhash_checksum_fasta.cpp -o bamhash_checksum_fasta.o
RUN g++ -std=c++11 -pthread -I. -Wno-deprecated-declarations -I/usr/local//include -O3 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=0 -DSEQAN_HAS_ZLIB=1 -c bamhash_checksum_fastq.cpp -o bamhash_checksum_fastq.o
RUN g++ -std=c++11 -pthread -o bamhash_checksum_bam bamhash_checksum_common.o bamhash_checksum_bam.o -L/usr/local/lib -lhts -lz -lssl -lcrypto -Wl,-rpath,/usr/local/lib
RUN g++ -std=c++11 -pthread -o bamhash_checksum_fasta bamhash_checksum_common.o bamhash_checksum_fasta.o -L/usr/local/lib -lhts -lz -lssl -lcrypto -Wl,-rpath,/usr/local/lib
RUN g++ -std=c++11 -pthread -o bamhash_checksum_fastq bamhash_checksum_common.o bamhash_checksum_fastq.o -L/usr/local/lib -lhts -lz -lssl -lcrypto -Wl,-rpath,/usr/local/lib

ENV PATH="/BamHash-1.2:${PATH}"