Python pip 常用指令

pip list    列出安裝清單
pip install :pacakagename:    安裝    
pip install -v :packagename:==1.0 安裝指定版本
pip install -U :pacakagename:    更新
pip uninstall :pacakagename:    移除
pip install -r :requirements.txt:    安裝清單
pip freeze > :requirements.txt:        輸出清單

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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