生信软件安装
一、安装trinity报错
解压代码:
tar -zxvf trinityrnaseq-v2.14.0.FULL_with_extendedTestData.tar.gz
进入软件文件夹
cd trinityrnaseq-v2.14.0/
然后输入make
进行安装,发现报错。
Using gnu compiler for Inchworm and Chrysalis
cd Inchworm && make
make[1]: Entering directory '/home/bio_kang/software/trinityrnaseq-v2.14.0/Inchworm'
mkdir -p build
cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && make DESTDIR=../ install
/bin/sh: 1: cmake: not found
make[1]: *** [Makefile:3: all] Error 127
make[1]: Leaving directory '/home/bio_kang/software/trinityrnaseq-v2.14.0/Inchworm'
make: *** [Makefile:32: inchworm_target] Error 2
二、解决报错
找不到cmake
命令,需要下载cmake,点击这里进行下载,选择适合自己的版本
使用下列命令进行解压(不要直接复制我的)
tar -zxvf cmake-3.23.2-linux-x86_64.tar.gz
进入~/.bashrc
文件,将下列代码添加到最后一行(:号后填自己文件的绝对路径):
export PATH=$PATH:/home/bio_kang/software/cmake/bin
输入cmake --version
查看是否安装成功
cmake version 3.23.2
然后在进入trinity目录下,使用make
命令
编译成功后使用Trinity --version
检查是否安装成功,发现又报错:
Command 'Trinity' not found, but can be installed with:
sudo apt install trinityrnaseq
在网上找了人家的参考,发现是还要进入相关文件进行编译,可以去参考小zi竹
写的
cd Inchworm/build/
rm CMakeCache.txt
make
然后继续进行安装,发现还是使用不了:
Trinity --version
Command 'Trinity' not found, but can be installed with:
sudo apt install trinityrnaseq
一直下载不成功,还找不到错误,勇敢放弃,删除.tar.gz文件后,使用conda进行下载(建议新建环境,以免出现不兼容的现象)
conda create -n trinity
然后输入Y,即可创建成功
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate trinity
#
# To deactivate an active environment, use
#
# $ conda deactivate
激活环境(最好新建一个环境!!!)conda activate trinity
查看版本信息:
Trinity --version
Trinity version: Trinity-v2.8.5
** NOTE: Latest version of Trinity is Trinity-v2.14.0, and can be obtained at:
https://github.com/trinityrnaseq/trinityrnaseq/releases