refactor: move dockerfile.1 to dockerfile

no need to keep old one around

rnaseq/ccbr_clear/Dockerfile

@@ -5,6 +5,12 @@ RUN mkdir -p /opt2
 
 RUN apt-get update && apt-get install -y zlib1g zlib1g-dev git build-essential
 
+# # INSTALL CLEAR
+# WORKDIR /opt2
+# RUN git clone https://github.com/YangLab/CLEAR
+# WORKDIR /opt2/CLEAR
+# RUN python ./setup.py install
+
 # Adding dependencies
 # Circexplorer2
 # Circexplorer2 --> UCSC dependencies
@@ -15,45 +21,36 @@ ADD gtfToGenePred /opt2
 ADD genePredToGtf /opt2
 RUN chmod a+rx gtfToGenePred genePredToGtf
 ENV PATH="/opt2:$PATH"
-# Circexplorer2 --> bowtie
-ADD bowtie-1.1.2.tar.gz /opt2
-ENV PATH="/opt2/bowtie-1.1.2:$PATH"
-# Circexplorer2 --> UCSC bedtools tophat 
-RUN apt-get install -y bedtools
-# Circexplorer2 --> UCSC tophat 
-ADD tophat-2.1.0.Linux_x86_64.tar.gz /opt2
-ENV PATH="/opt2/tophat-2.1.0.Linux_x86_64:$PATH"
+# Circexplorer2 --> UCSC bedtools tophat
+RUN apt-get install -y bedtools tophat bowtie
 # Circexplorer2 --> UCSC boostlibraries cufflinks
 RUN apt-get install -y libboost1.67-tools-dev
 # wget http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz
 ADD cufflinks-2.2.1.Linux_x86_64.tar.gz /opt2
+# WORKDIR /opt2
+# RUN tar -zxvf cufflinks-2.2.1.Linux_x86_64.tar.gz && \
+#     rm -rf cufflinks-2.2.1.Linux_x86_64.tar.gz
 ENV PATH="/opt2/cufflinks-2.2.1.Linux_x86_64:$PATH"
 RUN pip install docopt scipy
 RUN pip install circexplorer2
 
 # Adding HISAT2
-ADD hisat2-2.1.0.tar.gz /opt2
-ENV PATH="/opt2/hisat2-2.1.0:$PATH"
+ADD hisat2-2.2.1.tar.gz /opt2
+ENV PATH="/opt2/hisat2-2.2.1:$PATH"
 
 # Adding StringTie
 ADD stringtie-2.1.4.Linux_x86_64.tar.gz /opt2
-ENV PATH="/opt2/stringtie-2.1.4.Linux_x86_64:$PATH"
+ENV PATH="stringtie-2.1.4.Linux_x86_64:$PATH"
 
 # INSTALL CLEAR in conda environment
-# RUN . /opt/conda/etc/profile.d/conda.sh && \
-#     conda create -n clear python=2.7 && \
-# 	conda activate clear && \
-# 	pip install pybedtools==0.8.1 && \
-# 	python -m pip install git+https://github.com/YangLab/CLEAR.git
-# RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
-#     echo "conda activate clear" >> ~/.bashrc
-# # SHELL ["conda", "run", "-n", "clear", "/bin/bash", "-c"]
-
-# # INSTALL CLEAR
-WORKDIR /opt2
-RUN git clone https://github.com/YangLab/CLEAR
-WORKDIR /opt2/CLEAR
-RUN python ./setup.py install
+RUN . /opt/conda/etc/profile.d/conda.sh && \
+    conda create -n clear python=2.7 && \
+	conda activate clear && \
+	pip install pybedtools==0.8.1 && \
+	python -m pip install git+https://github.com/YangLab/CLEAR.git
+RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
+    echo "conda activate clear" >> ~/.bashrc
+# SHELL ["conda", "run", "-n", "clear", "/bin/bash", "-c"]
 
 RUN chmod -R a+rX /opt2
 WORKDIR /data2