docker-ichor

FROM dhspence/docker-baseimage:031822

MAINTAINER David Spencer dspencer@wustl.edu

LABEL Image for basic ad-hoc bioinformatic analyses

install hmmcopy

RUN apt-get update && apt-get install cmake
build-essential
fort77
xorg-dev
liblzma-dev
libblas-dev
gfortran
gcc-multilib
gobjc++
aptitude
libreadline-dev
libpcre3 libpcre3-dev --no-install-recommends -y &&
cd /opt/ &&
git config --global http.sslVerify false &&
git clone --recursive https://github.com/shahcompbio/hmmcopy_utils.git &&
cd /opt/hmmcopy_utils &&
cmake . &&
make &&
cp bin/* /usr/local/bin/

install R

ARG R_VERSION ARG BUILD_DATE ENV BUILD_DATE 2017-06-20 ENV R_VERSION=${R_VERSION:-3.5.0} RUN cd /tmp/ &&
## Download source code curl -O https://cran.r-project.org/src/base/R-3/R-${R_VERSION}.tar.gz &&
## Extract source code tar -xf R-${R_VERSION}.tar.gz &&
cd R-${R_VERSION} &&
## Set compiler flags R_PAPERSIZE=letter &&
R_BATCHSAVE="--no-save --no-restore" &&
R_BROWSER=xdg-open &&
PAGER=/usr/bin/pager &&
PERL=/usr/bin/perl &&
R_UNZIPCMD=/usr/bin/unzip &&
R_ZIPCMD=/usr/bin/zip &&
R_PRINTCMD=/usr/bin/lpr &&
LIBnn=lib &&
AWK=/usr/bin/awk &&
CFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" &&
CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" &&
## Configure options ./configure --enable-R-shlib
--enable-memory-profiling
--with-readline
--with-blas="-lopenblas"
--disable-nls
--with-x=no
--without-recommended-packages &&
## Build and install make &&
make install &&
## Add a default CRAN mirror echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')" >> /usr/local/lib/R/etc/Rprofile.site &&
## Add a library directory (for user-installed packages) mkdir -p /usr/local/lib/R/site-library &&
chown root:staff /usr/local/lib/R/site-library &&
chmod g+wx /usr/local/lib/R/site-library &&
## Fix library path echo "R_LIBS_USER='/usr/local/lib/R/site-library'" >> /usr/local/lib/R/etc/Renviron &&
echo "R_LIBS=${R_LIBS-'/usr/local/lib/R/site-library:/usr/local/lib/R/library:/usr/lib/R/library'}" >> /usr/local/lib/R/etc/Renviron &&
## Use littler installation scripts Rscript -e "install.packages(c('littler', 'docopt'))" &&
ln -s /usr/local/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r &&
ln -s /usr/local/lib/R/site-library/littler/examples/installGithub.r /usr/local/bin/installGithub.r &&
ln -s /usr/local/lib/R/site-library/littler/bin/r /usr/local/bin/r

RUN Rscript -e "source('https://bioconductor.org/biocLite.R'); biocLite('HMMcopy'); biocLite('GenomeInfoDb'); install.packages(c('devtools','optparse'))" RUN Rscript --default-packages=devtools -e "install_github('broadinstitute/ichorCNA', '--no-docs')"

RUN cd /opt/ && wget https://github.com/broadinstitute/ichorCNA/archive/master.zip &&
unzip master.zip && mv ichorCNA-master/scripts/*.R /usr/local/bin/ && rm -Rf master.zip ichorCNA-master

Clean up

RUN cd / &&
rm -rf /tmp/* &&
apt-get autoremove -y &&
apt-get autoclean -y &&
rm -rf /var/lib/apt/lists/* &&
apt-get clean