simplified Dockerfile; fixed varscan version

build/Dockerfile

@@ -11,26 +11,20 @@ RUN apt-get update && apt-get install -y \
 
 # Create a new source directory
 WORKDIR /home
-RUN mkdir varscan-src
 RUN mkdir exec
-WORKDIR /home/varscan-src
 
 # get varscan 
-RUN git clone https://github.com/dkoboldt/varscan.git
-
-# Move varscan.jar (allow for version updates) to /home/exec directory
-RUN rm varscan/VarScan.*source.jar
-RUN mv varscan/VarScan.v2.*.jar /home/exec/VarScan.jar
+RUN wget  -O /home/exec/VarScan.jar https://github.com/dkoboldt/varscan/releases/download/2.4.2/VarScan.v2.4.2.jar
 
 # R and DNAcopy package (move to R library location)
 # NOTE: this is NOT a stable way of doing this, bioconductor updates this package regularly
-RUN wget -O /home/exec/DNAcopy_1.42.0.tar.gz http://www.bioconductor.org/packages/release/bioc/src/contrib/DNAcopy_1.44.0.tar.gz
+RUN wget -O /home/exec/DNAcopy_1.42.0.tar.gz http://www.bioconductor.org/packages/release/bioc/src/contrib/DNAcopy_1.46.0.tar.gz
 
 # Samtools 0.1.18 - note: 0.1.19 and 1.1 do NOT work, VarScan copynumber dies on the mpileup
 RUN wget http://downloads.sourceforge.net/project/samtools/samtools/0.1.18/samtools-0.1.18.tar.bz2
 RUN tar -xvf samtools-0.1.18.tar.bz2
 # the make command generates a lot of warnings, none of them relevant to the final samtools code, hence 2>/dev/null
-WORKDIR /home/varscan-src/samtools-0.1.18
+WORKDIR /home/samtools-0.1.18
 RUN make DFLAGS='-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0' LIBCURSES='' 2>/dev/null 
 RUN mv samtools /home/exec
 
@@ -41,5 +35,5 @@ RUN chmod -R 777 /home/exec
 WORKDIR /home
 
 # And clean up
-RUN apt-get clean && rm -rf /var/lib/apt/lists/* /home/varscan-src
+RUN apt-get clean && rm -rf /var/lib/apt/lists/* /home/samtools*