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;

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};