生信软件的安装

centos上安装，anaconda3
在python2.7的环境下
SRA-tools v2.9.0 (https://github.com/ncbi/sratoolkit)
parallel-fastq-dump v0.6.3 (https://github.com/rvalieris/parallel-fastq-dump)

conda install parallel-fastq-dump

BBTools v38.32 (https://sourceforge.net/projects/bbmap/)
Lighter v1.1.2 (https://github.com/mourisl/Lighter)

 git clone https://github.com/mourisl/Lighter.git
cd Lighter
make

Minia v3.2 (https://github.com/GATB/minia)

# get a local copy of minia source code
git clone --recursive https://github.com/GATB/minia.git

# compile the code an run a simple test on your computer
cd minia
sh INSTALL

安装后，使用/minia/build/bin/./minia即可
也可加入环境变量
Redundans v0.14c (https://github.com/lpryszcz/redundans)

git clone --recursive https://github.com/lpryszcz/redundans.git
chmod -R 777 redundans/
cd redundans && bin/.compile.sh

Minimap2 v2.12 (https://github.com/lh3/minimap2)

conda install minimap2

Samtools v1.9 (http://www.htslib.org/)
BESST v2.2.8 (https://github.com/ksahlin/BESST)

sudo easy_install BESST
# 另一种方法
pip install BESST
#  另一种
 

GapCloser v1.12 (http://soap.genomics.org.cn/)
BUSCO v3.0.2 (http://busco.ezlab.org/)

 conda install busco

MAFFT v7.407 (https://mafft.cbrc.jp/alignment/software/)

conda install MAFFT

trimAl v1.4.1 (http://trimal.cgenomics.org/)

conda install trimal

FASconCAT-G v1.04 (https://github.com/PatrickKueck/FASconCAT-G)
PHYLUCE v1.6.6 (http://phyluce.readthedocs.io/en/latest/index.html)

conda install phyluce

faToTwoBit (http://hgdownload.soe.ucsc.edu/admin/exe/)

conda install ucsc-fatotwobit

ART-20160605 (https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm)
Stampy v1.0.32 (http://www.well.ox.ac.uk/project-stampy)
SeqKit v0.9.3 (https://github.com/shenwei356/seqkit)

conda install -c bioconda seqkit

bedtools

sudo apt-get install bedtools

BBmap

conda install BBmap

fastp

conda install fastp

bioawk

conda install bioawk

pip卸载包使用的是

pip uninstall bioawk

安装AMAS

conda install amas
# 使用
AMAS.py -h