appelmar

FROM rocker/r-devel:latest
RUN apt update && apt install -y git flex
RUN git clone git://gcc.gnu.org/git/gcc.git gcc11
RUN cd gcc11 && ./contrib/download_prerequisites 
RUN mkdir gcc-build && cd gcc-build && ../gcc11/configure -disable-multilib --enable-languages=c,c++,fortran
RUN cd gcc-build && make -j4 && make install

RUN echo 'LD_LIBRARY_PATH="/usr/local/lib64:${R_LD_LIBRARY_PATH}:${LD_LIBRARY_PATH}"' >> /usr/lib/R/etc/ldpaths
RUN mkdir ~/.R && echo 'CXX11=/usr/local/bin/g++' > ~/.R/Makevars && echo 'CXX=/usr/local/bin/g++' >> ~/.R/Makevars && echo 'CC=/usr/local/bin/gcc' >> ~/.R/Makevars
RUN echo 'CCFLAGS = -Wall -pedantic -O2' >> ~/.R/Makevars && echo 'CXXFLAGS = -Wall -pedantic -O2' >> ~/.R/Makevars && echo 'CXX11FLAGS = -Wall -pedantic -O2' >> ~/.R/Makevars 

jefferis

library(flycircuit)
# download NBLAST all by all score matrix (used e.g. for hierarchical clustering)
# this downloads a single 2Gb file to your machine as a one-off
fc_download_data('http://flybrain.mrc-lmb.cam.ac.uk/si/nblast/flycircuit/allbyallblastcv4.5.ff',
  type='ff')
# set that as default all by all score matrix
options('flycircuit.scoremat'="allbyallblastcv4.5.ff")

# load neuron list 
# the actual neuron data will be downloaded and cached to your machine on demand