issue with installation

[skatragadda-nygc]

Here is my Dockerfile

FROM ubuntu:latest

# Get all apt dependencies
RUN apt update
RUN apt install -y software-properties-common
RUN apt update

RUN apt install -y python-dev \
libbz2-dev \
gcc-7 \
libgmp3-dev \
build-essential \
zlib1g-dev \
libncurses5-dev \
libncursesw5-dev \
liblzma-dev \
libhts-dev \
libboost-all-dev \
cmake \
git \
libgmp-dev \
python3 \
wget

RUN wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 -O htslib.tar.bz2
RUN tar -xjvf htslib.tar.bz2
RUN cd htslib-1.9 && make && make install
RUN cd ..

# Install Octopus
RUN git clone -b master https://github.com/luntergroup/octopus.git
RUN apt install -y curl
RUN octopus/scripts/install.py --install-dependencies --download-forests --threads 4

Hello,

We ran into following issues during the installation step while trying to create docker image. Would you know how to resolve this?

build 19-Mar-2020 19:39:14 [ 39%] Building CXX object src/CMakeFiles/octopus.dir/core/callers/cell_caller.cpp.o build 19-Mar-2020 19:39:33 src/CMakeFiles/octopus.dir/build.make:1574: recipe for target 'src/CMakeFiles/octopus.dir/core/callers/cancer_caller.cpp.o' failed build 19-Mar-2020 19:39:33 c++: internal compiler error: Killed (program cc1plus) build 19-Mar-2020 19:39:33 Please submit a full bug report, build 19-Mar-2020 19:39:33 with preprocessed source if appropriate. build 19-Mar-2020 19:39:33 See file:///usr/share/doc/gcc-7/README.Bugs for instructions. build 19-Mar-2020 19:39:33 make[2]: [src/CMakeFiles/octopus.dir/core/callers/cancer_caller.cpp.o] Error 4 build 19-Mar-2020 19:39:33 make[2]: Waiting for unfinished jobs.... build 19-Mar-2020 19:39:47 make[1]: [src/CMakeFiles/octopus.dir/all] Error 2 build 19-Mar-2020 19:39:47 CMakeFiles/Makefile2:275: recipe for target 'src/CMakeFiles/octopus.dir/all' failed build 19-Mar-2020 19:39:47 Makefile:129: recipe for target 'all' failed build 19-Mar-2020 19:39:47 make: [all] Error 2 build 19-Mar-2020 19:40:44 No bin directory found, making one build 19-Mar-2020 19:40:44 Installing Octopus 0.6.3-beta (master fd981298) build 19-Mar-2020 19:40:44 No forest directory found, making one build 19-Mar-2020 19:40:44 Downloading https://storage.googleapis.com/luntergroup/octopus/forests/germline.v0.6.3-beta.forest to /octopus/resources/forests/germline.v0.6.3-beta.forest build 19-Mar-2020 19:40:44 Downloading https://storage.googleapis.com/luntergroup/octopus/forests/somatic.v0.6.3-beta.forest to /octopus/resources/forests/somatic.v0.6.3-beta.forest build 19-Mar-2020 19:40:45 Removing intermediate container ff7a1d3dd769 error 19-Mar-2020 19:40:45 The command '/bin/sh -c octopus/scripts/install.py --install-dependencies --download-forests --threads 4' returned a non-zero code: 2

Thanks in Advance Sri

[dancooke]

Could be that your Docker container ran out of memory. Try building with a single thread (i.e. change --threads 4 to --threads 1), or increasing memory to the container.

[skatragadda-nygc]

Thanks for your response. We see new error message now

usage: install.py [-h] [--prefix PREFIX] [-D] [--clean] [-c C_COMPILER] [-cxx CXX_COMPILER] [--keep_cache] [--debug] [--sanitize] [--static] [--threads THREADS] [--boost BOOST] [--htslib HTSLIB] [--gmp GMP] [-F] [--verbose] install.py: error: unrecognized arguments: --install-dependencies --download-forests

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[skatragadda-nygc]

Changing branch to master from developer this time

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[skatragadda-nygc]

It worked this time on a vm with big memory. Thanks for your help!

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[dancooke]

No problem.