diff --git a/CHANGELOG.md b/CHANGELOG.md index 3bcbbdf..0b0606c 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/dockers/centos7/Dockerfile b/dockers/centos7/Dockerfile index e24e8fb..f68a039 100644 --- a/dockers/centos7/Dockerfile +++ b/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 \ No newline at end of file