Fixed centos7 docker for pandoc and boost

CHANGELOG.md

@@ -3,6 +3,7 @@
 ## [Upcoming]
 ### Changed
 * Config field "Estimation/Merge/barcodes_file" now accepts paths, relative to config directory, as well as path with "~/"
+* Fixed bug with several files passed to `-r` option of dropest (Issue #25)
 ### Added
 * To improve reproducibility, config file is now copied to log directory
 * 'Directional' UMI correction can be applied during dropEst phase with "-u" option. In this case, information for more 

dockers/centos7/Dockerfile

@@ -2,33 +2,26 @@ FROM library/centos:7.4.1708
 MAINTAINER Viktor Petukhov "viktor.s.petuhov@ya.ru"
 
 RUN \
-  yum install -y wget && \
-  wget http://repo.enetres.net/enetres.repo -O /etc/yum.repos.d/enetres.repo && \
-  wget ftp://fr2.rpmfind.net/linux/Mandriva/official/2010.0/x86_64/media/main/release/lib64icu42-4.2.1-1mdv2010.0.x86_64.rpm && \
-  rpm -ivh lib64icu42-4.2.1-1mdv2010.0.x86_64.rpm && \
   yum -y install epel-release && \
   yum -y install \
-    boost-devel \
+    bzip2-devel \
     cmake \
     cmake3 \
     git \
     libcurl-devel \
-    libpng-devel \
-    libX11-devel \
-    mesa-libGL-devel \
-    mesa-libGLU-devel \
     openssl-devel \
-    R-3.4.1 \
+    R \
     vim \
-    xorg-x11-server-Xorg \
-    xorg-x11-server-Xorg-devel
+    wget
 
-RUN \ 
-    cd /root && \
-    git clone git://github.com/pezmaster31/bamtools.git && \
-    mkdir -p bamtools/build && \
-    cd bamtools/build && \
-    cmake3 .. && make && make install
+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 && \
+  cmake3 .. && make && make install
 
 RUN useradd -m user
 USER user
@@ -37,16 +30,28 @@ ENTRYPOINT ["/bin/bash"]
 WORKDIR /home/user
 
 RUN \
+  mkdir ~/local && \
+  wget http://sourceforge.net/projects/boost/files/boost/1.60.0/boost_1_60_0.tar.gz && \
+  tar -xvzf boost_1_60_0.tar.gz && \
+  cd boost_1_60_0 && \
+  ./bootstrap.sh --with-libraries=filesystem,iostreams,log,system,thread,test && \
+  ./b2 cxxflags=-std=c++11 link=shared threading=multi install --prefix=/home/user/local
+
+RUN \
+  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 \
-  cd && \
-  mkdir -p ~/dropEst/build && \
-  cd ~/dropEst/build && \
-  cmake3 .. && make
+  mkdir dropEst/build && \
+  cd dropEst/build && \
+  cmake -D BOOST_ROOT=~/local/ .. && \
+  make
 
-ENV PATH=/home/user/dropEst/build:$PATH
+ENV PATH=/home/user/dropEst/build:$PATH