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modified: .gitignore new file: data/cds/sp_chlorodb/parameters.sh deleted: data/ir/LSC_RefDB.fasta deleted: data/ir/SSC_RefDB.fasta modified: detectors/cds/bin/go_cds.sh modified: detectors/normalize/lib/lookforIR.lib.sh modified: detectors/normalize/lib/selectIR.py modified: organnot/Dockerfile new file: organnot/README.md new file: organnot/dorgannot deleted: ports/.DS_Store deleted: src/ncbiblast/binaries/.gitignore deleted: src/prokov/lxpack/tests/S.fasta deleted: src/prokov/lxpack/tests/St.fasta deleted: src/prokov/lxpack/tests/Stt.fasta deleted: src/prokov/lxpack/tests/aS.fasta deleted: src/prokov/lxpack/tests/aSt.fasta deleted: src/prokov/lxpack/tests/aStt.fasta deleted: src/prokov/lxpack/tests/aaS.fasta deleted: src/prokov/lxpack/tests/aaSt.fasta deleted: src/prokov/lxpack/tests/aaStt.fasta new file: src/repseek/repseek-2014.09.tgz
65 lines
1.5 KiB
Docker
65 lines
1.5 KiB
Docker
FROM ubuntu:jammy AS builder
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LABEL dockerfile.version="1"
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LABEL software="phyloskims"
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##
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#
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# Install org-annot
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#
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##
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WORKDIR /
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RUN apt-get update --fix-missing && apt upgrade -y
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RUN apt-get install -y build-essential
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RUN apt-get install -y git tcsh bash gawk parallel gettext zlib1g-dev libglib2.0-0
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RUN git clone https://github.com/PhyloSkims/annotate.git org-annotate
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#
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# Compile tools
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#
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WORKDIR /org-annotate/src
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RUN make
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##
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#
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# Install Organelle Assembler
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#
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##
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# WORKDIR "/"
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# RUN apt install -y python3-pip python3-dev python3-venv
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# RUN git clone https://git.metabarcoding.org/org-asm/org-asm.git
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# RUN python3 -m venv org-assembler
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# WORKDIR "/org-asm"
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# RUN bash -c '../org-assembler/bin/pip3 install -r requirements.txt'
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# RUN bash -c '../org-assembler/bin/python3 setup.py install --no-serenity'
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# WORKDIR "/"
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##
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#
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# Install the final image grouping previously compiled softwares
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#
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##
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FROM ubuntu:jammy AS phyloskims
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WORKDIR /
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RUN apt update --fix-missing && apt upgrade -y
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RUN apt-get install -y tcsh bash gawk parallel zlib1g libglib2.0-0 clustalo muscle cd-hit hmmer
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COPY --from=builder /org-annotate /org-annotate
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RUN rm -rf /org-annotate/src
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# COPY --from=builder /org-assembler /org-assembler
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# COPY --from=builder /org-assembler/bin/oa /bin
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COPY organnot /bin
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RUN chmod +x /bin/organnot
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#
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# Recompile HMMER models
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#
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WORKDIR /org-annotate/data/its/ITSx_db/HMMs
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RUN rm *.h3*
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RUN for f in *.hmm ; do hmmpress $f ; done
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WORKDIR /
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RUN mkdir -p /data
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WORKDIR /data |