How to add git repo path in the Dockerfile?

Can someone please tell me how to add the git repo path in the Dockerfile. Here is my Docker file

FROM ubuntu:14.04.3
MAINTAINER Upendra Devisetty

RUN apt-get update && apt-get install -y g++ \
            make \
            git \
            zlib1g-dev \
            python \
            wget \
            curl \
            python-matplotlib \
            python-numpy \
            python-pandas


ENV BINPATH /usr/bin
RUN git clone https://upendra_35@bitbucket.org/upendra_35/evolinc_docker.git
RUN chmod +x /evolinc_docker/evolinc-part-I.sh && cp /evolinc_docker/evolinc-part-I.sh $BINPATH

RUN wget -O- http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz | tar xzvf -
RUN wget -O- https://github.com/TransDecoder/TransDecoder/archive/2.0.1.tar.gz | tar xzvf -
RUN wget -O- http://seq.cs.iastate.edu/CAP3/cap3.linux.x86_64.tar | tar vfx -
RUN curl ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-x64-linux.tar.gz > ncbi-blast-2.3.0+-x64-linux.tar.gz
RUN tar xvf ncbi-blast-2.3.0+-x64-linux.tar.gz
RUN wget https://www.python.org/ftp/python/2.7.10/Python-2.7.10.tgz
RUN tar -zxvf Python-2.7.10.tgz
RUN cd Python-2.7.10 && ./configure && make
RUN cd ..
RUN wget -O- http://ftp.mirrorservice.org/sites/download.sourceforge.net/pub/sourceforge/q/qu/quast/quast-3.0.tar.gz | tar zxvf -
RUN wget http://sourceforge.net/projects/bio-bwa/files/latest/download?source=files && tar xvf download\?source\=files
RUN cd bwa-0.7.12 && make
RUN cd ..

ENV PATH /cufflinks-2.2.1.Linux_x86_64/:$PATH
ENV PATH /TransDecoder-2.0.1/:$PATH
ENV PATH /CAP3/:$PATH
ENV PATH /ncbi-blast-2.3.0+/bin/:$PATH
ENV PATH /Python-2.7.10/:$PATH
ENV PATH /bedtools2-2.25.0/bin/:$PATH
ENV PATH /samtools-bcftools-htslib-1.0_x64-linux/bin/:$PATH
ENV PATH /bwa-0.7.12/:$PATH

ENTRYPOINT ["/usr/bin/evolinc-part-I.sh"]
CMD ["-h"]

When i run this

  • Deploying multicontainer docker environment (flask & nginx) with EBS
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  • docker run --rm -v $(pwd):/working-dir -w /working-dir ubuntu/evolinc -c AthalianaslutteandluiN30merged.gtf -g TAIR10_chr.fasta -r TAIR10_cdna_20110103_representative_gene_model_updated.fa -b TE_RNA_transcripts.fa -t AnnotatedPEATPeaks.gff -x Atha_known_lncRNAs.mod.gff
    

    I’m getting this error

    python: can't open file 'get_gene_length_filter.py': [Errno 2] No such file or directory
    

    What i don’t understand is how do i add the git rep to the path so that all the scripts in the repo can be opened.

  • docker postgres pgadmin local connection
  • MongoDb docker hangs after some requests
  • Can't pull kubernetes dns container from behind proxy
  • Docker MySQL ERROR 1049 (42000): Unknown database 'users'
  • Managing Spring Cloud Dataflow Server logs
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  • One Solution collect form web for “How to add git repo path in the Dockerfile?”

    You are doing RUN git clone https://upendra_35@bitbucket.org/upendra_35/evolinc_docker.git without ever specifying where it will be cloned.

    Same for the wget commands.

    You might want to set a WORKDIR first instead of dumping everything in, by default, /. See Dockerfile WORKDIR.

    Your script evolinc-part-I.sh might expect to find those resource in a specific path: if you were able to make that script work in your local machine (without docker), compare with your image by running a container with a bash, to explore what was installed where.

    Docker will be the best open platform for developers and sysadmins to build, ship, and run distributed applications.