gene-is 도커 파일

# gene-is를 돌리기 위한 도커 파일임.
FROM ubuntu:20.04

# 이상한 메세지 블락하기
ARG DEBIAN_FRONTEND=noninteractive

# 패키지 업데이트
# ubuntu에 기본적으로 필요한거 외에 devtools를 설치하기 위한 프로그램들 설치
RUN apt-get update && apt update
RUN apt-get install -y build-essential
RUN apt-get install -y cmake zlib1g-dev wget git libncurses-dev 
RUN apt-get install -y libz-dev liblzma-dev libbz2-dev g++
RUN apt-get install -y libcurl4-gnutls-dev libxml2-dev libssl-dev libfontconfig1-dev
RUN apt-get install -y libharfbuzz-dev libfribidi-dev
RUN apt-get install -y libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev
# 파이썬 설치부분 (없으면 아까우니 넣음.
RUN apt-get -y install python3 python
RUN apt-get -y install python3-pip python3-distutils
RUN apt-get -y install zip

# Working directory 설정
WORKDIR /home

# 프로그램 설치
# BEDTOOLS 설치
RUN mkdir /home/Bedtools && cd /home/Bedtools
RUN wget https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/bedtools/BEDTools.v2.17.0.tar.gz
RUN tar -zxvf BEDTools.v2.17.0.tar.gz && cd bedtools-2.17.0 && make
RUN cp bin/* /usr/local/bin/

# BWA
RUN mkdir /home/BWA && cd /home/BWA
RUN wget https://sourceforge.net/projects/bio-bwa/files/bwa-0.7.4.tar.bz2 && tar -xf bwa-0.7.4.tar.bz2
RUN cd bwa-0.7.4 && make && make install
RUN export PATH=$PATH:/home/BWA/bwa-0.7.4 && cp /home/BWA/bwa-0.7.4/bwa /usr/local/bin/bwa

# Samtools
RUN mkdir /home/Samtools && cd /home/Samtools
RUN wget https://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2 && tar -xf samtools-0.1.19.tar.bz2
RUN cd samtools-0.1.19 && make
RUN export PATH=$PATH:/home/Samtools/samtools-0.1.19 && cp /home/Samtools/samtools-0.1.19/samtools /usr/local/bin/samtools

# BLAT v.35
RUN mkdir /home/Blat && cd /home/Blat
RUN apt-get install unzip
RUN wget http://users.soe.ucsc.edu/~kent/src/blatSrc35.zip && unzip blatSrc35.zip
#RUN MACHTYPE=x86_64-pc-linux-gnu  && export MACHTYPE
RUN MACHTYPE=x86_64 && export MACHTYPE
RUN mkdir -p ~/bin/x86_64/
RUN export PATH=~/bin/x86_64::$PATH
RUN cd blatSrc && make

# GENE is
RUN apt-get install -y vim
RUN mkdir /home/Gene-is && cd /home/Gene-is
RUN git clone https://github.com/G100DKFZ/gene-is.git && cd gene-is
RUN export GENIS=/home/Gene-is/gene-is

 

이후에 설정파일들을 조정해준다.

BLAT의 경우는 그냥 쓰면 에러가 걸린다. 사실 뭘 해도 에러가 걸리는거 같기도하다.

vim $GENIS/configFile_targetedSequencing_pairedEnd.txt

#############################################################################
##                      Third-party tools
#Provide path to these third-party tools
#############################################################################
#Provide path to the BWA aligner
#aligner     = $GENIS/tools/bin/bwa
aligner = /usr/local/bin/bwa
#############################################################################
#Path to the secondary aligner. (BLAT)
#megaAligner = megablast
#blatAligner =  $GENIS/tools/bin/blat
blatAligner = ~/bin/x86_64/blat

#Path to the BLAT indexed file of refernce genome and vector.
genomeVectorIndexBlat=$GENIS/test/datasets/testGenomeVector.fa.2bit

#Path to the trimming and filtering tool (Skewer)
skewer = $GENIS/tools/bin/skewer

#Path to the Samtools
#samtools= $GENIS/tools/bin/samtools
samtools= /usr/local/bin/samtools

#Path to the bedtools
#bedTools= $GENIS/tools/bin/bedtools
bedTools= /usr/local/bin/bedtools