《学习小组Day3笔记--云小医》

---linux环境下的软件安装---

一、安装miniconda

1. 查看需要的安装版本

bio14@VM-0-6-ubuntu:~$ uname -a
Linux VM-0-6-ubuntu 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
bio14@VM-0-6-ubuntu:~$

2. 选定安装目录

cd biosoft
cd ~/biosoft

3. 获取下载链接

清华大学开源软件镜像站

4.下载miniconda到本地

• wget Linux下开发的开放源代码的软件；wget [参数列表] [目标软件、网页的网址]
• wget https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-latest-Linux-x86_64.sh

「for Windows」请记住这里的粘贴不是ctrl+c和ctrl+V了，选中，鼠标左键点一下是复制，右键点一下是粘贴；
「for Mac」直接cmd + c 复制，cmd + v粘贴

# 执行下载
yunyi_inn@DESKTOP-FJH1CT1:~/biosoft$ wget https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-latest-Linux-x86_64.sh
#下载完成
yunyi_inn@DESKTOP-FJH1CT1:~/biosoft$ ls
Miniconda3-latest-Linux-x86_64.sh

5. 进行安装

• bash Miniconda3-latest-Linux-x86_64.sh

yunyi_inn@DESKTOP-FJH1CT1:~/biosoft$ bash Miniconda3-latest-Linux-x86_64.sh
...
...
Thank you for installing Miniconda3!

6. 进行激活

• source ~/.bashrc

yunyi_inn@DESKTOP-FJH1CT1:~/biosoft$ conda
conda: command not found
yunyi_inn@DESKTOP-FJH1CT1:~/biosoft$ source ~/.bashrc
(base) yunyi_inn@DESKTOP-FJH1CT1:~/biosoft$ conda
...
...
(base) yunyi_inn@DESKTOP-FJH1CT1:~/biosoft$

7. 添加镜像

所谓镜像网站，相当于主网站的副本，conda在国外，我们在国内下载软件速度会很慢，因此配置镜像，从镜像网站下载，可以加快下载速度。

# 使用中科大的镜像
conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda/
conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/
conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/free/
conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/main/
conda config --set show_channel_urls yes

二、使用conda

1. 查看当前用户安装的软件列表

• conda list

(base) yunyi_inn@DESKTOP-FJH1CT1:~/biosoft$ conda list
# packages in environment at /home/yunyi_inn/miniconda3:
#
# Name                    Version                   Build  Channel
...
...

2. 安装软件

• 最新版本命令：conda install fastqc -y 【-y是yes】
• 特定版本命令：conda install fastqc=0.11.7 -y

安装命令含有 -y

(base) yunyi_inn@DESKTOP-FJH1CT1:~/biosoft$ conda install fastqc
Collecting package metadata (current_repodata.json): -
|
done
Solving environment: done

安装命令没有 -y

(base) yunyi_inn@DESKTOP-FJH1CT1:~/biosoft$ conda install fastqc
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##

  environment location: /home/yunyi_inn/miniconda3

  added / updated specs:
    - fastqc


The following NEW packages will be INSTALLED:

  dbus               anaconda/pkgs/main/linux-64::dbus-1.13.18-hb2f20db_0
  expat              anaconda/pkgs/main/linux-64::expat-2.4.4-h295c915_0
  fastqc             anaconda/cloud/bioconda/noarch::fastqc-0.11.9-hdfd78af_1
  font-ttf-dejavu-s~ anaconda/pkgs/main/noarch::font-ttf-dejavu-sans-mono-2.37-hd3eb1b0_0
  fontconfig         anaconda/pkgs/main/linux-64::fontconfig-2.13.1-h6c09931_0
  freetype           anaconda/pkgs/main/linux-64::freetype-2.11.0-h70c0345_0
  glib               anaconda/pkgs/main/linux-64::glib-2.69.1-h4ff587b_1
  icu                anaconda/pkgs/main/linux-64::icu-58.2-he6710b0_3
  libpng             anaconda/pkgs/main/linux-64::libpng-1.6.37-hbc83047_0
  libuuid            anaconda/pkgs/main/linux-64::libuuid-1.0.3-h7f8727e_2
  libxcb             anaconda/pkgs/main/linux-64::libxcb-1.14-h7b6447c_0
  libxml2            anaconda/pkgs/main/linux-64::libxml2-2.9.12-h03d6c58_0
  openjdk            anaconda/pkgs/main/linux-64::openjdk-11.0.13-h87a67e3_0
  pcre               anaconda/pkgs/main/linux-64::pcre-8.45-h295c915_0
  perl               anaconda/pkgs/main/linux-64::perl-5.26.2-h14c3975_0


Proceed ([y]/n)?

3. 确认fastqc软件是否安装成功

• 帮助文档 fastqc --help

(base) yunyi_inn@DESKTOP-FJH1CT1:~/biosoft$ fastqc --help

            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

DESCRIPTION
...
...

4. 卸载软件

• 命令：conda remove fastqc -y

(base) yunyi_inn@DESKTOP-FJH1CT1:~/biosoft$ conda remove fastqc -y

三、conda安装环境

1. 查看当前工作环境

• 命令： conda info --envs (前面带*的就是默认的)

(base) yunyi_inn@DESKTOP-FJH1CT1:~/biosoft$ conda info --envs
# conda environments:
#
base                  *  /home/yunyi_inn/miniconda3

(base) yunyi_inn@DESKTOP-FJH1CT1:~/biosoft$

2. 建立新工作环境

• rnaseq的conda环境：指定python版本是3，并安装软件fastqc、trimmomatic
• conda create -n rna-seq python=3 fastqc trimmomatic -y

(base) yunyi_inn@DESKTOP-FJH1CT1:~/biosoft$ conda create -n rna-seq python=3 fastqc trimmomatic -y
Collecting package metadata (current_repodata.json): -
done
Solving environment: done
...

3. 激活新的conda环境

• conda activate rna-seq

(base) yunyi_inn@DESKTOP-FJH1CT1:~/biosoft$ conda activate rna-seq

4. 查看当前默认工作环境

• conda info --envs
• *已经显示为 rna-seq

(rna-seq) yunyi_inn@DESKTOP-FJH1CT1:~/biosoft$ conda info --envs
# conda environments:
#
base                     /home/yunyi_inn/miniconda3
rna-seq               *  /home/yunyi_inn/miniconda3/envs/rna-seq