title: Can't open file when i try to run a shell script inside Docker container
body: <p>I have been struggling this for a while and i don't know what i am doing wrong. I am trying to run a shell script inside a container and the shell script reads a python script from the directory where the shell script is located. But i am getting this error saying `python: can't open file 'get_gene_length_filter.py': [Errno 2] No such file or directory'. </p>
  
  <p>Here is my Dockerfile:</p>
  
  <pre><code>FROM ubuntu:14.04.3
  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
  ENV EVO2GIT https://upendra_35@bitbucket.org/upendra_35/evolinc_docker.git
  RUN git clone $EVO2GIT
  WORKDIR /evolinc_docker
  RUN chmod +x evolinc-part-I.sh &amp;&amp; cp 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 -
  
  ENV PATH /evolinc_docker/cufflinks-2.2.1.Linux_x86_64/:$PATH
  ENV PATH /evolinc_docker/TransDecoder-2.0.1/:$PATH
  ENTRYPOINT ["/usr/bin/evolinc-part-I.sh"]
  CMD ["-h"]
  </code></pre>
  
  <p>Here is my git repo code:</p>
  
  <pre><code>#!/bin/bash
  # Create a directory to move all the output files
  mkdir output
  # Extracting classcode u transcripts, making fasta file, removing transcripts &gt; 200 and selecting protein coding transcripts
  grep '"u"' $comparefile | gffread -w transcripts_u.fa -g $referencegenome - &amp;&amp; python get_gene_length_filter.py transcripts_u.fa \
      transcripts_u_filter.fa &amp;&amp; TransDecoder.LongOrfs -t transcripts_u_filter.fa
  </code></pre>
  
  <p>And this is how i'm running it:</p>
  
  <pre><code>docker run --rm -v $(pwd):/working-dir -w /working-dir ubuntu/evolinc -c AthalianaslutteandluiN30merged.gtf -g TAIR10_chr.fasta  
  </code></pre>