安裝 SAIGE

安裝 SAIGE v0.45

https://github.com/weizhouUMICH/SAIGE

1.設定 Python 2.7.17 環境
pip install cget

2. R
install.packages("R.utils", "Rcpp", "RcppParallel", "RcppArmadillo", "data.table", "RcppEigen", "Matrix", "methods", "BH", "optparse", "SPAtest", "SKAT","devtools")
devtools::install_github("leeshawn/MetaSKAT")

devtools::install_github("weizhouUMICH/SAIGE")
下載失敗可先將檔案下載後安裝
src_branch=master
repo_src_url=https://github.com/weizhouUMICH/SAIGE
git clone --depth 1 -b $src_branch $repo_src_url
R CMD INSTALL --library=path_to_final_SAIGE_library SAIGE

其他
1.安裝時會連上網路下載檔案
2. http://zlib.net/zlib-1.2.11.tar.gz 連結已變更 https://zlib.net/fossils/zlib-1.2.11.tar.gz會造成安裝失敗

Debian 11 安裝 tabix , samtools

 apt install  tabix samtools

PLINK107 安裝

 !/bin/bash

# install PLINK 1.07
# https://zzz.bwh.harvard.edu/plink/download.shtml

src=https://zzz.bwh.harvard.edu/plink/dist/plink-1.07-x86_64.zip
target=/opt/PLINK107

[ $(which busybox) ]&& { for i in wget unzip;do [ -f "/usr/local/bin/${i}" ] || ln -s $(which busybox) /usr/local/bin/${i}; done; };

for i in unzip wget;do [ $(which ${i}) ]&& : || { echo check ${i}: not found ${i}! &&exit 1; } ;done;

[ -d "$target" ]&&mv ${target} ${target}.$(date +%Y-%m-%d-%H-%M);

mkdir -p $target;cd $target;

echo $target >readme.txt;echo $src >>readme.txt

wget -q -O- $src | unzip -;

chmod a+x plink;cd -;

for i in plink;do [ -f "/usr/local/bin/${i}" ]&&mv /usr/local/bin/${i} /usr/local/bin/${i}.$(date +%Y-%m-%d-%H-%M); ln -s ${target}/${i} /usr/local/bin/${i}07;done;

PLINK 1.90 安裝

 !/bin/bash
# install PLINK 1.90 beta
#https://www.cog-genomics.org/plink/

src=https://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20210606.zip
target=/opt/PLINK190b

[ $(which busybox) ]&& { for i in wget unzip;do [ -f "/usr/local/bin/${i}" ] || ln -s $(which busybox) /usr/local/bin/${i}; done; };

for i in unzip wget;do [ $(which ${i}) ]&& : || { echo check ${i}: not found ${i}! &&exit 1; } ;done;

[ -d "$target" ]&&mv ${target} ${target}.$(date +%Y-%m-%d-%H-%M);

mkdir -p $target;cd $target;

echo $target >readme.txt;echo $src >>readme.txt

wget -q -O- $src | unzip -;

chmod a+x plink;cd -;

for i in plink;do [ -f "/usr/local/bin/${i}" ]&&mv /usr/local/bin/${i} /usr/local/bin/${i}.$(date +%Y-%m-%d-%H-%M);   ln -s ${target}/${i} /usr/local/bin/${i};done;

DReichLab / EIG 安裝摘要(debian 10)

target=/opt

src=https://github.com/DReichLab/EIG/archive/v7.2.1.tar.gz

apt-get install -y libgsl0-dev libopenblas-dev gfortran liblapacke-dev

pwd=$(pwd)

cd $target

wget -O- $src |tar zxv

cd EIG-7.2.1/src

sed  -i 's/# override LDLIBS += -llapacke/override LDLIBS += -llapacke/g' Makefile

make

make install

cd $pwd

for i in $(find ${target}/EIG-7.2.1/bin/ -type f  -perm /a=x);do ln -s $i /usr/local/bin/$(basename $i);done;

EIGENSOFT 安裝摘要

apt-get install -y libgsl0-dev libopenblas-dev gfortran liblapacke-dev
wget https://storage.googleapis.com/broad-alkesgroup-public/EIGENSOFT/EIG-6.1.4.tar.gz

安裝 RTG Tools

#!/bin/bash
# RTG Tools
# https://github.com/RealTimeGenomics/rtg-tools

apt install -y ant
target=/opt
cd $target
git clone https://github.com/RealTimeGenomics/rtg-tools.git
cd rtg-tools
ant runalltests
ant zip-nojre
cd $target
unzip ${target}/rtg-tools/dist/*
                              

安裝 vcflib

Debian/Ubuntu
apt-get install libvcflib-tools libvcflib-dev

by source
#!/bin/bash
#https://github.com/vcflib/vcflib

target=/opt
pwd=$(pwd)
apt install -y git make cmake libbz2-dev liblzma-dev libc6-dev
cd $target
git clone --recursive https://github.com/vcflib/vcflib.git
cd vcflib
make -j
cd bin
for i in $(find ${target}/vcflib/bin/ -type f  -perm /a=x);do ln -s $i /usr/local/bin/$(basename $i);done;
cd $pwd

安裝 vcftools

 #!/bin/bash
# http://vcftools.sourceforge.net/

src=https://nchc.dl.sourceforge.net/project/vcftools/vcftools_0.1.13.tar.gz?viasf=1
target=/opt
pwd=$(pwd)
mkdir -p ${target}
cd $target
wget -O- $src |tar zx
cd vcftools_0.1.13
make
cd bin
for i in $(find ${target}/vcftools_0.1.13/bin/ -type f  -perm /a=x);do ln -s $i /usr/local/bin/$(basename $i);done;
cd $pwd

安裝 bcftools

 #!/bin/bash
# install  bcftools
# https://samtools.github.io/bcftools/

pwd=$(pwd);
target=/opt/
cd ${target};
apt install -y git automake libgsl-dev libcurl4-openssl-dev
git clone --recurse-submodules git://github.com/samtools/htslib.git

git clone git://github.com/samtools/bcftools.git
cd bcftools
# The following is optional:
#autoheader && autoconf && ./configure --enable-libgsl --enable-perl-filters
make
ln -s ${target}/bcftools/bcftools /usr/local/bin/bcftools
cd ${pwd};

安裝 plink 2

 #!/bin/bash
# install PLINK 2.00 alpha
# https://www.cog-genomics.org/plink/2.0/

src=http://s3.amazonaws.com/plink2-assets/alpha2/plink2_linux_x86_64.zip
src=https://s3.amazonaws.com/plink2-assets/plink2_linux_x86_64_20211125.zip
target=/opt/PLINK2a

[ $(which busybox) ]&& { for i in wget unzip;do [ -f "/usr/local/bin/${i}" ] || ln -s $(which busybox) /usr/local/bin/${i}; done; };
for i in unzip wget;do [ $(which ${i}) ]&& : || { echo check ${i}: not found ${i}! &&exit 1; } ;done;
[ -d "$target" ]&&mv ${target} ${target}.$(date +%Y-%m-%d-%H-%M);
mkdir -p $target;cd $target;
echo $target >readme.txt;echo $src >>readme.txt
wget -q -O- $src | unzip -;
chmod a+x plink2;cd -;
for i in plink2;do [ -f "/usr/local/bin/${i}" ]&&mv /usr/local/bin/${i} /usr/local/bin/${i}.$(date +%Y-%m-%d-%H-%M);   ln -s ${target}/${i} /usr/local/bin/${i};done;
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