Trinity安装全过程并解决部分报错

简单的安装方式：

# Hompage : https://github.com/trinityrnaseq/trinityrnaseq/wiki

# 安装
sudo apt-get install trinityrnaseq

# 报错
# E: 无法修正错误，因为您要求某些软件包保持现状，就是它们破坏了软件

# 解决一: 安装指定版本的被依赖包


# 解决方法二: 使用aptitude进行安装，aptitude 会对依赖关系进行智能处理
sudo apt-get install aptitude
sudo aptitude install <package name>

官网的安装方式：

# https://github.com/trinityrnaseq/trinityrnaseq/wiki/Installing-Trinity
Additional tools required for running Trinity include:

    bowtie2
    jellyfish
    salmon
    samtools
# 上面4个软件需要提前安装


sudo wget https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v2.12.0/trinityrnaseq-v2.12.0.FULL.tar.gz

tar -xf trinityrnaseq-v2.12.0.FULL.tar.gz 
cd trinityrnaseq-v2.12.0/
make

# 报错 No CMAKE_CXX_COMPILER could be found.
# 解决 
sudo apt-get install -y build-essential


#报错：
seqtk.c:31:10: fatal error: zlib.h: No such file or directory
   31 | #include <zlib.h>
      |          ^~~~~~~~
# 解决：
sudo apt-get install zlib1g-dev

# 报错
autoheader: command not found
# 解决
apt-get install autoconf


#报错 ：Building HTSlib requires libbzip2 development files to be installed on the
# build machine; you may need to ensure a package such as libbz2-dev (on Debian
# or Ubuntu Linux) or bzip2-devel (on RPM-based Linux distributions or Cygwin)
# is installed.
# 解决：
sudo apt install libbz2-dev

# Building HTSlib requires liblzma development files to be installed on the
# build machine; you may need to ensure a package such as liblzma-dev (on Debian
# or Ubuntu Linux), xz-devel (on RPM-based Linux distributions or Cygwin), or
# xz (via Homebrew on macOS) is installed; or build XZ Utils from source.
# 解决：
sudo apt install liblzma-dev


# 将可执行文件添加进PATH环境变量

# Assemble RNA-Seq data like so:
 Trinity --seqType fq --left reads_1.fq --right reads_2.fq --CPU 6 --max_memory 20G 

安装依赖软件

# bowtie2
# http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#building-from-source
wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.4.4/bowtie2-2.4.4-source.zip

unzip bowtie2-2.4.4-source.zip
make
make static-libs && make STATIC_BUILD=1
make sra-deps && make USE_SRA=1 	# supports aligning SRA reads
# configure: error: required ngs-sdk package not found
将安装目录添加进PATH变量

# 安装jellyfish
wget https://github.com/gmarcais/Jellyfish/releases/download/v2.3.0/jellyfish-2.3.0.tar.gz
sudo tar -xf jellyfish-2.3.0.tar.gz
cd jellyfish-2.3.0
./configure 
sudo make
sudo make install
将安装目录添加进PATH变量

# 报错： jellyfish: error while loading shared libraries: libjellyfish-2.0.so.2: cannot open shared object file: No such file or directory
export LD_LIBRARY_PATH="/usr/local/lib

# samtools
sudo apt install samtools

# salmon
sudo apt install salmon

# 依赖的R包
install.packages('BiocManager')
library(BiocManager)
install('edgeR')

# /usr/bin/ld: cannot find -llapack
# /usr/bin/ld: cannot find -lblas
# /usr/bin/ld: cannot find -lgfortran

sudo apt install liblapacke-dev
sudo apt install libblas-dev
sudo apt install libgfortran-dev



install('ctc')
# /bin/bash: gfortran: command not found
sudo apt-get install gfortran

install('Biobase')
install('ape')
install.packages('gplots')