生信星球学习day3
学习内容
安装miniconda3、安装软件、环境
一、安装miniconda3
#下载miniconda3
wget https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-latest-Linux-x86_64.sh```
#安装，一路按enter或yes
bash Miniconda3-latest-Linux-x86_64.sh
#加入环境变量
echo 'export PATH=~/miniconda3/bin:$PATH' >> ~/.bashrc
#刷新
source ~/.bashrc
#验证
conda
#出现以下内容，说明安装成功
usage: conda [-h] [-V] command ...
conda is a tool for managing and deploying applications, environments and packages.
Options:
positional arguments:
command
clean Remove unused packages and caches.
compare Compare packages between conda environments.
config Modify configuration values in .condarc. This is modeled after the git config command.
Writes to the user .condarc file (/home/bio05/.condarc) by default.
create Create a new conda environment from a list of specified packages.
help Displays a list of available conda commands and their help strings.
info Display information about current conda install.
init Initialize conda for shell interaction. [Experimental]
install Installs a list of packages into a specified conda environment.
list List linked packages in a conda environment.
package Low-level conda package utility. (EXPERIMENTAL)
remove Remove a list of packages from a specified conda environment.
uninstall Alias for conda remove.
run Run an executable in a conda environment. [Experimental]
search Search for packages and display associated information. The input is a MatchSpec, a
query language for conda packages. See examples below.
update Updates conda packages to the latest compatible version.
upgrade Alias for conda update.
optional arguments:
-h, --help Show this help message and exit.
-V, --version Show the conda version number and exit.
conda commands available from other packages:
env
二、安装软件
#添加频道， 使用清华镜像，可提高软件下载速度
bio05@VM-0-6-ubuntu:~/biosoft$ conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
du.cn/anaconda/cloud/bioconda
conda config --set show_channel_urls yesbio05@VM-0-6-ubuntu:~/biosoft$ conda config --add channels https://oud/conda-forgeinghua.edu.cn/anaconda/clo
bio05@VM-0-6-ubuntu:~/biosoft$ conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
bio05@VM-0-6-ubuntu:~/biosoft$ conda config --set show_channel_urls yes
#查看软件列表
bio05@VM-0-6-ubuntu:~/biosoft$ conda list
# packages in environment at /home/bio05/miniconda3:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main defaults
brotlipy 0.7.0 py38h27cfd23_1003 defaults
ca-certificates 2020.10.14 0 defaults
certifi 2020.6.20 pyhd3eb1b0_3 defaults
cffi 1.14.3 py38h261ae71_2 defaults
chardet 3.0.4 py38h06a4308_1003 defaults
#搜索fastqc软件
bio05@VM-0-6-ubuntu:~/biosoft$ conda search fastqc
Loading channels: done
# Name Version Build Channel
fastqc 0.11.7 pl5.22.0_0 anaconda/cloud/bioconda
fastqc 0.11.7 pl5.22.0_2 anaconda/cloud/bioconda
fastqc 0.11.8 0 anaconda/cloud/bioconda
fastqc 0.11.8 1 anaconda/cloud/bioconda
fastqc 0.11.8 2 anaconda/cloud/bioconda
fastqc 0.11.9 0 anaconda/cloud/bioconda
fastqc 0.11.9 hdfd78af_1 anaconda/cloud/bioconda
#安装fastqc
bio05@VM-0-6-ubuntu:~/biosoft$ conda install fastqc -y
#验证是否安装成功
bio05@VM-0-6-ubuntu:~/biosoft$ fastqc -h
FastQC - A high throughput sequence QC analysis tool
SYNOPSIS
fastqc seqfile1 seqfile2 .. seqfileN
fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam]
[-c contaminant file] seqfile1 .. seqfileN
#卸载fastqc
bio05@VM-0-6-ubuntu:~/biosoft$ conda remove fastqc -y
#直到出现
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#验证是否卸载完成
bio05@VM-0-6-ubuntu:~/biosoft$ fastqc -h
-bash: /home/bio05/miniconda3/bin/fastqc: No such file or directory #卸载成功
三、环境
#查看环境
bio05@VM-0-6-ubuntu:~/biosoft$ conda info --envs
# conda environments:
#
base * /home/bio05/miniconda3
#新建一个叫“rna-seq”的环境，python版本为3，同时安装fastqc和trimmomatic软件
bio05@VM-0-6-ubuntu:~/biosoft$ conda create -n rna-seq python=3 fastqc trimmomatic -y
#查看新环境是否建立成功
bio05@VM-0-6-ubuntu:~/biosoft$ conda info --envs
# conda environments:
#
base * /home/bio05/miniconda3
rna-seq /home/bio05/miniconda3/envs/rna-seq
#激活新环境，使用conda activate不能成功激活，使用source activate激活，前面出现(rna-seq)说明激活成功
bio05@VM-0-6-ubuntu:~/biosoft$ source activate rna-seq
#查看fastqc是否成功安装，出现很多帮助信息，安装成功
(rna-seq) bio05@VM-0-6-ubuntu:~/biosoft$ fastqc -h
FastQC - A high throughput sequence QC analysis tool
SYNOPSIS
fastqc seqfile1 seqfile2 .. seqfileN
fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam]
[-c contaminant file] seqfile1 .. seqfileN
#转换环境
(rna-seq) bio05@VM-0-6-ubuntu:~/biosoft$ source activate base
(base) bio05@VM-0-6-ubuntu:~/biosoft$ conda deactivate
#退出环境
(rna-seq) bio05@VM-0-6-ubuntu:~/biosoft$ conda deactivate
bio05@VM-0-6-ubuntu:~/biosoft$
