forked from tohsumi-repare/cca
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathDockerfile
48 lines (39 loc) · 2.88 KB
/
Dockerfile
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
#################################
# docker build -t icrsc/icr-cca .
# docker run --rm -it -v ./login/temp:/home:rw tohsumirepare/cca crisprCountsAnalysis COUNTS=noClone.txt REPMAP=noClone.repmap OUT_MAX=noclone
# docker run --rm -it -v ./login/temp:/home:rw tohsumirepare/cca crisprCountsAnalysis COUNTS=noClone.txt REPMAP=noClone.repmap OUT=noclone
# docker run --rm -it -v ./login/temp2:/home icrsc/icr-cca crisprCountsAnalysis COUNTS=noClone.txt REPMAP=noClone.repmap OUT_MAX=noclone
# docker run --rm -it -v ./login/temp2:/home icrsc/icr-cca crisprCountsAnalysis COUNTS=noClone.txt REPMAP=noClone.repmap OUT=noClone
#sudo rm -rf login/temp/cca_files
#sudo rm -rf login/temp2/cca_files
#################################
#FROM ubuntu:latest
#FROM ubuntu:20.04
FROM rocker/r-ver:4.3.2
ENV DEBIAN_FRONTEND=noninteractive
RUN apt-get update
RUN apt-get install -y --no-install-recommends apt-transport-https software-properties-common dirmngr gpg-agent
RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
#RUN add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'
#RUN apt-get update && apt-get install -y --no-install-recommends build-essential gfortran libblas-dev liblapack-dev libz-dev bwa wget r-base libpng-dev imagemagick
RUN apt-get update && apt-get install -y --no-install-recommends build-essential gfortran libblas-dev liblapack-dev libz-dev bwa wget libpng-dev imagemagick
#RUN Rscript -e "install.packages('rspm') ; rspm::enable()"
RUN Rscript -e "install.packages('ggplot2')"
RUN Rscript -e "install.packages('fitdistrplus')"
RUN Rscript -e "install.packages('classInt')"
RUN Rscript -e "install.packages('actuar')"
RUN Rscript -e "install.packages('stringr')"
RUN Rscript -e "install.packages('dplyr')"
RUN Rscript -e "install.packages('PRROC')"
RUN Rscript -e "install.packages('BiocManager')"
RUN Rscript -e "BiocManager::install('ComplexHeatmap')"
RUN mkdir /root/data
ADD data /root/data/
RUN mkdir /root/doc
RUN mkdir /root/src
ADD src /root/src/
RUN g++ -Wall -std=c++17 -I /root/src/alglib_include -O3 -DDEBUG -I /root -lz -pthread /root/src/Projects/Repare/ccaGatherQC.cpp -o /usr/local/bin/ccaGatherQC
RUN g++ -Wall -std=c++17 -I /root/src/alglib_include -O3 -DDEBUG -I /root -lz -pthread /root/src/Projects/Repare/cleanUpCca.cpp -o /usr/local/bin/cleanUpCca
RUN g++ -Wall -std=c++17 -I /root/src/alglib_include -O3 -DDEBUG -I /root -lz -pthread /root/src/Projects/Repare/crisprCountsAnalysis.cpp -o /usr/local/bin/crisprCountsAnalysis
RUN g++ -Wall -std=c++17 -I /root/src/alglib_include -O3 -DDEBUG -I /root -lz -pthread /root/src/Projects/Repare/barplotGenesFromCcaFoldchange.cpp -o /usr/local/bin/barplotGenesFromCcaFoldchange
RUN g++ -Wall -std=c++17 -I /root/src/alglib_include -O3 -DDEBUG -I /root -lz -pthread /root/src/Projects/Repare/convertCrisprFastqsToReadCountFile.cpp -o /usr/local/bin/convertCrisprFastqsToReadCountFile