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alinux.sh
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sudo -s
#library
yum update && yum -y remove java-1.7.0-openjdk* && yum -y install zlib-devel git bzip2-devel xz-devel python-pip fuse java-1.8.0-openjdk*
curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.rpm.sh | sudo bash && yum -y install git-lfs
mkdir -p /Pipeline/01.software
mkdir -p /Pipeline/02.resource
#BWA
cd /Pipeline/01.software && git clone https://github.com/lh3/bwa
cd bwa && make
ln -s /Pipeline/01.software/bwa/bwa /usr/bin/
#Samtools
cd /Pipeline/01.software && git clone https://github.com/samtools/htslib.git
cd /Pipeline/01.software && git clone https://github.com/samtools/samtools.git
cd /Pipeline/01.software/samtools && make
ln -s /Pipeline/01.software/samtools/samtools /usr/bin/
#GATK
cd /Pipeline/01.software && git clone https://github.com/broadinstitute/gatk.git
cd /Pipeline/01.software/gatk/ && ./gradlew installAll
ln -s /Pipeline/01.software/gatk/gatk /usr/bin/
#Picard
cd /Pipeline/01.software && git clone https://github.com/broadinstitute/picard.git
cd /Pipeline/01.software/picard/ && ./gradlew shadowJar
#Golang
mkdir -p /Pipeline/01.software/go
cd /Pipeline/01.software/go && echo 'export GOPATH='`pwd` >> ~/.bashrc && source ~/.bashrc
wget https://dl.google.com/go/go1.12.5.linux-amd64.tar.gz && tar -C `pwd` -xzf go1.12.5.linux-amd64.tar.gz
echo 'export PATH=$PATH:/Pipeline/01.software/go/go/bin/' >> ~/.bashrc && source ~/.bashrc
#goofys
mkdir -p $GOPATH/src/golang.org/x/ && cd $GOPATH/src/golang.org/x/
git clone https://github.com/golang/net.git $GOPATH/src/golang.org/x/net
git clone https://github.com/golang/text.git $GOPATH/src/golang.org/x/text
git clone https://github.com/golang/sys.git $GOPATH/src/golang.org/x/sys
git clone https://github.com/golang/crypto.git $GOPATH/src/golang.org/x/crypto
git clone https://github.com/grpc/grpc-go.git $GOPATH/src/google.golang.org/grpc
go get -u github.com/golang/protobuf/{proto,protoc-gen-go}
git clone https://github.com/google/go-genproto.git $GOPATH/src/google.golang.org/genproto
cd $GOPATH/src/
go install google.golang.org/grpc
git clone https://github.com/golang/sync.git $GOPATH/src/golang.org/x/sync
git clone https://github.com/golang/oauth2.git $GOPATH/src/golang.org/x/oauth2
git clone https://github.com/googleapis/google-api-go-client.git $GOPATH/src/google.golang.org/api
go install google.golang.org/api
go install net #need fuse lib #yum install fuse -y
go get github.com/kahing/goofys && go install github.com/kahing/goofys
echo 'export PATH=$PATH:/Pipeline/01.software/go/bin/' >> ~/.bashrc && source ~/.bashrc