Fixed centos6 docker for pandoc and new R

dockers/centos6/Dockerfile

@@ -4,27 +4,25 @@ MAINTAINER Viktor Petukhov "viktor.s.petuhov@ya.ru"
 RUN \
   yum -y install epel-release && \
   yum -y install \
-    boost-devel \
+    bzip2-devel \
     centos-release-scl \
     cmake \
     cmake3 \
     git \
     libcurl-devel \
-    libpng-devel \
-    libX11-devel \
-    mesa-libGL-devel \
-    mesa-libGLU-devel \
     openssl-devel \
-    R-3.4.1 \
+    R \
     vim \
-    wget \
-    xorg-x11-server-Xorg \
-    xorg-x11-server-Xorg-devel && \
-  yum install -y devtoolset-4-gcc* && \
-  scl enable devtoolset-4 bash
+    wget
+
+RUN yum -y install devtoolset-6-gcc*
+
+RUN source /opt/rh/devtoolset-6/enable
 
 RUN \
   cd /root && \
+  wget https://github.com/jgm/pandoc/releases/download/2.1.3/pandoc-2.1.3-linux.tar.gz && \
+  tar xvzf pandoc-2.1.3-linux.tar.gz --strip-components 1 -C /usr/local/ && \
   git clone git://github.com/pezmaster31/bamtools.git && \
   mkdir bamtools/build && \
   cd bamtools/build && \
@@ -33,31 +31,33 @@ RUN \
 RUN useradd -m user
 USER user
 
-ENV PATH="/opt/rh/devtoolset-4/root/usr/bin/:$PATH"
-
-ENTRYPOINT ["scl", "enable", "devtoolset-4", "bash"]
 WORKDIR /home/user
 
+RUN echo "source /opt/rh/devtoolset-6/enable" > ~/.bashrc
+
 RUN \
+  source ~/.bashrc && \
+  mkdir ~/local && \
   wget http://sourceforge.net/projects/boost/files/boost/1.55.0/boost_1_55_0.tar.gz && \
   tar -xvzf boost_1_55_0.tar.gz && \
   cd boost_1_55_0 && \
   ./bootstrap.sh --with-libraries=filesystem,iostreams,log,system,thread,test && \
-  mkdir ~/local
-
-RUN \
-  cd boost_1_55_0 && \
   ./b2 cxxflags=-std=c++11 link=shared threading=multi install --prefix=/home/user/local
 
 RUN \
+  source ~/.bashrc && \
   cd && \
+  git clone https://github.com/VPetukhov/ks.git && \
   git clone https://github.com/hms-dbmi/dropEst.git && \
   mkdir -p ~/R/x86_64-redhat-linux-gnu-library/3.4 && \
-  R -e 'chooseCRANmirror(ind=52); install.packages(c("devtools"), lib = "~/R/x86_64-redhat-linux-gnu-library/3.4")' && \
+  echo '.libPaths(c("~/R/x86_64-redhat-linux-gnu-library/3.4", .libPaths()))' > .Rprofile && \
+  R -e 'chooseCRANmirror(ind=52); install.packages(c("devtools"))' && \
+  R -e 'devtools::install_local("~/ks/")' && \
   R -e 'devtools::install_local("~/dropEst/dropestr/", dependencies=T)' && \
   R -e 'chooseCRANmirror(ind=52); install.packages(c("Rcpp","RcppEigen", "RInside", "Matrix", "optparse", "rmarkdown"))'
 
 RUN \
+  source ~/.bashrc && \
   mkdir dropEst/build && \
   cd dropEst/build && \
   cmake -D BOOST_ROOT=~/local/ .. && \