title: How to add git repo path in the Dockerfile?
body: <p>Can someone please tell me how to add the git repo path in the Dockerfile. Here is my Docker file</p>
  
  <pre><code>FROM ubuntu:14.04.3
  MAINTAINER Upendra Devisetty
  
  RUN apt-get update &amp;&amp; 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 &amp;&amp; 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 &gt; 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 &amp;&amp; ./configure &amp;&amp; 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 &amp;&amp; tar xvf download\?source\=files
  RUN cd bwa-0.7.12 &amp;&amp; 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"]
  </code></pre>
  
  <p>When i run this </p>
  
  <pre><code>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
  </code></pre>
  
  <p>I'm getting this error</p>
  
  <pre><code>python: can't open file 'get_gene_length_filter.py': [Errno 2] No such file or directory
  </code></pre>
  
  <p>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.</p>