dockerfile and changed path for cummerbund script to make them wor to…

…ghether

Dockerfile

@@ -1,18 +1,15 @@
-FROM ubuntu:latest
+FROM ubuntu:14.04
 
-RUN echo "deb http://archive.ubuntu.com/ubuntu" `lsb_release -a | grep Codename | awk '{print $2}'` "multiverse main" > /etc/apt/sources.list.d/archive.list
+ARG DEBIAN_FRONTEND=noninteractive
 
-RUN apt-get -y update && apt-get install -y bowtie2
+ADD https://raw.githubusercontent.com/cyverseuk/tuxedo/master/cummerbund_plot_scripts.r /usr/local/bin/
 
-RUN apt-get -y install software-properties-common samtools tophat cufflinks r-base r-bioc-cummerbund
+ADD https://raw.githubusercontent.com/cyverseuk/tuxedo/master/rna_seq_4_conditions_docker.py /usr/local/bin/
 
-COPY cummerbund_plot_scripts.r /usr/local/bin/
-
-COPY rna_seq_4_conditions_docker.py /usr/local/bin/
-
-RUN chmod +x /usr/local/bin/rna_seq_4_conditions_docker.py
-
-RUN chmod +x /usr/local/bin/cummerbund_plot_scripts.r
+RUN echo "deb http://archive.ubuntu.com/ubuntu/ trusty multiverse" >> /etc/apt/sources.list && \
+	apt-get update -y && apt-get -yy install bowtie2 software-properties-common samtools tophat cufflinks r-base r-bioc-cummerbund && \
+	chmod +x /usr/local/bin/rna_seq_4_conditions_docker.py && \
+    	chmod +x /usr/local/bin/cummerbund_plot_scripts.r
 
 ENTRYPOINT ["python3", "/usr/local/bin/rna_seq_4_conditions_docker.py"]
 

rna_seq_4_conditions_docker.py

@@ -277,11 +277,11 @@
 #-------------------------------------------- CummeRbund ------------------------------------------------------
 
 if not os.path.exists("./r_plots"): os.mkdir("./r_plots")
-plot_script = "Rscript /cummerbund_plot_scripts.r"
+plot_script = "Rscript /usr/local/bin/cummerbund_plot_scripts.r"
 
 os.system(plot_script)
 
 #-------------------------------------------- Cleaning ------------------------------------------------------
 
 os.system("rm -r ./assembled_transcripts ./condition* ./file.txt")
-os.system("mkdir -p ./index_files/; mv %s* ./index_files" %args.indpre)
+os.system("mkdir -p ./index_files/; mv %s* ./index_files" %args.indpre)