plachta11b/motifsim repository overview

FROM ubuntu:20.04 AS library

RUN find / -name libstdc++.so.6
RUN find / -name libgomp.so.1

# wget http://motifsim.org/download/motifsim_v2-2-linux64
ADD ./add/ /

ENV DEBIAN_FRONTEND "noninteractive"
RUN apt-get update && apt purge -y python-is-python2 && apt-get install -y \
	libgomp1 \
	g++ \
	r-base \
	python3 \
	python3-pip \
	python-is-python3 \
	ghostscript \
	&& rm -rf /var/lib/apt/lists/*

# ggplot2 ggdendro dendextend ape | there is suppressMessages on require so missing dependency does not throw error
# this does not produce any files and tmp is empty - The downloaded source packages are in '/tmp/RtmpSRuTMK/downloaded_packages'
RUN R -e "install.packages(c('ggplot2', 'ggdendro', 'dendextend', 'ape'), repos = 'http://cran.us.r-project.org')"
RUN pip3 install numpy

RUN ldd /packages/motifsim_v2-2-linux64
# linux-vdso.so.1 (0x00007ffedcc8b000)
# libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f7df9e92000)
# libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f7df9d43000)
# libgomp.so.1 => /lib/x86_64-linux-gnu/libgomp.so.1 (0x00007f7df9d01000)
# libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f7df9ce6000)
# libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f7df9cc3000)
# libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f7df9ad1000)
# /lib64/ld-linux-x86-64.so.2 (0x00007f7dfa077000)
# libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f7df9ac9000)

RUN mkdir -p /packages/motifsim
WORKDIR /packages/motifsim/

RUN unzip -q ../motifsim_v2-2.zip
RUN cp -r /packages/motifsim/weblogo-3.4 /weblogo-3.4

# remove hardcoded path rewriting user input
RUN sed -i 's| outputPath = inputPath.substr(0, inputPath.length() - 7) + "result/";||' main.cpp
RUN for file in *.cpp; do sed -i "s/\"Invalid input path or file name.\"/\"$file: Invalid input path or file name.\"/g" $file; done
RUN for file in *.cpp; do sed -i "s|inputPath.substr(0, inputPath.length() - 7) + \"|\"/|g" $file; done
RUN for file in *.cpp; do sed -i "s|\" + cwd + \"/prince.php|/packages/motifsim/prince.php|g" $file; done
RUN sed -i "s/\"readInputFile.cpp: Invalid input path or file name.\"/\"readInputFile.cpp: Invalid input path or file name.\" << (inputPath + inputFileName).c_str() /" readInputFile.cpp

RUN g++ -fopenmp *.cpp *.h -o /packages/motifsim_compiled_by_plachta


RUN apt-get update && apt-get install -y \
	php \
	&& rm -rf /var/lib/apt/lists/*

RUN ln -s /usr/bin/php /usr/bin/php5

RUN chmod +x /packages/motifsim_v2-2-linux64

ADD ./wrapper/ /wrapper

CMD [ "/packages/motifsim_compiled_by_plachta" ]

/wrapper/motifsim.sh --configuration $dataset/datalist --dataset-dir $dataset --result-dir $results_dir $motifsim_args
/wrapper/help.sh