学习小组Day3笔记—单双

主要学习内容：Linux系统的软件安装

第一步：登陆服务器（不用再登阿里云啦，还是不大理解我电脑里的的putty相当于什么，可以理解为是用来登陆服务器的助手吗，服务器是大家可以一起用但又互不干扰的一个超级大的计算机，然后这个计算机安的系统就是linux的。）

第二步：bzip2（理解为一款解压软件，给你的linux系统的电脑先安上它，再下载别的东西安装。）

bzip2
-bash: bzip2: command not found

yum install -y bzip2

Installed:
  bzip2.x86_64 0:1.0.6-13.el7

Complete!

第三步：安装和配置miniconda （再给你电脑安个应用商店，（miniconda——conda的精华版miniconda）
官网下载python3.6（计算机程序设计语言）对应的版本
复制网址（sh可能就当作exe）
下载

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

2018-08-22 21:18:21 (7.00 MB/s) - ‘Miniconda3-latest-Linux-x86_64.sh’ saved [58468498/58468498]

安装

bash Miniconda3-latest-Linux-x86_64.sh

enter

Do you accept the license terms? [yes|no]
[no] >>>
Please answer 'yes' or 'no':'
>>> yes

enter

installation finished.
Do you wish the installer to prepend the Miniconda3 install location
to PATH in your /root/.bashrc ? [yes|no]
[no] >>> yes

Thank you for installing Miniconda3!

激活

source ~/.bashrc
[root@shanshuang121 biosofe]# conda

命令行（[root@shanshuang121 biosofe]# 号后面就是）

添加国内镜像

conda config --add channels https://mirrors.ustc.edu.cn/anaconda/pkgs/free
conda config --add channels https://mirrors.ustc.edu.cn/anaconda/pkgs/main/
conda config --add channels https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/
conda config --add channels https://mirrors.ustc.edu.cn/anaconda/cloud/bioconda/
conda config --set show_channel_urls yes

第四步：使用miniconda搜索 安装卸载软件 （以fastqc为例）

查看软件列表

conda list
# packages in environment at /root/miniconda3:
#
# Name                    Version                   Build  Channel
asn1crypto                0.24.0                   py36_0    defaults
ca-certificates           2018.03.07                    0    defaults
certifi                   2018.4.16                py36_0    defaults
cffi                      1.11.5           py36h9745a5d_0    defaults
chardet                   3.0.4            py36h0f667ec_1    defaults
conda                     4.5.4                    py36_0    defaults
conda-env                 2.6.0                h36134e3_1    defaults
cryptography              2.2.2            py36h14c3975_0    defaults
idna                      2.6              py36h82fb2a8_1    defaults
libedit                   3.1.20170329         h6b74fdf_2    defaults
libffi                    3.2.1                hd88cf55_4    defaults
libgcc-ng                 7.2.0                hdf63c60_3    defaults
libstdcxx-ng              7.2.0                hdf63c60_3    defaults
ncurses                   6.1                  hf484d3e_0    defaults
openssl                   1.0.2o               h20670df_0    defaults
pip                       10.0.1                   py36_0    defaults
pycosat                   0.6.3            py36h0a5515d_0    defaults
pycparser                 2.18             py36hf9f622e_1    defaults
pyopenssl                 18.0.0                   py36_0    defaults
pysocks                   1.6.8                    py36_0    defaults
python                    3.6.5                hc3d631a_2    defaults
readline                  7.0                  ha6073c6_4    defaults
requests                  2.18.4           py36he2e5f8d_1    defaults
ruamel_yaml               0.15.37          py36h14c3975_2    defaults
setuptools                39.2.0                   py36_0    defaults
six                       1.11.0           py36h372c433_1    defaults
sqlite                    3.23.1               he433501_0    defaults
tk                        8.6.7                hc745277_3    defaults
urllib3                   1.22             py36hbe7ace6_0    defaults
wheel                     0.31.1                   py36_0    defaults
xz                        5.2.4                h14c3975_4    defaults
yaml                      0.1.7                had09818_2    defaults
zlib                      1.2.11               ha838bed_2    defaults

搜索fastqc软件

conda search fastqc
Loading channels: done
# Name                  Version           Build  Channel
fastqc                   0.10.1               0  anaconda/cloud/bioconda
fastqc                   0.10.1               1  anaconda/cloud/bioconda
fastqc                   0.11.2               1  anaconda/cloud/bioconda
fastqc                   0.11.2      pl5.22.0_0  anaconda/cloud/bioconda
fastqc                   0.11.3               0  anaconda/cloud/bioconda
fastqc                   0.11.3               1  anaconda/cloud/bioconda
fastqc                   0.11.4               0  anaconda/cloud/bioconda
fastqc                   0.11.4               1  anaconda/cloud/bioconda
fastqc                   0.11.4               2  anaconda/cloud/bioconda
fastqc                   0.11.5               1  anaconda/cloud/bioconda
fastqc                   0.11.5      pl5.22.0_2  anaconda/cloud/bioconda
fastqc                   0.11.5      pl5.22.0_3  anaconda/cloud/bioconda
fastqc                   0.11.6               2  anaconda/cloud/bioconda
fastqc                   0.11.6      pl5.22.0_0  anaconda/cloud/bioconda
fastqc                   0.11.6      pl5.22.0_1  anaconda/cloud/bioconda
fastqc                   0.11.7               4  anaconda/cloud/bioconda
fastqc                   0.11.7      pl5.22.0_0  anaconda/cloud/bioconda
fastqc                   0.11.7      pl5.22.0_2  anaconda/cloud/bioconda

安装

conda install fastqc -y

 conda install fastqc=0.11.7 -y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

卸载

conda remove fastqc -y

The following packages will be REMOVED:

    fastqc: 0.11.7-pl5.22.0_0 https://mirrors.ustc.edu.cn/anaconda/cloud/bioconda

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

第五步：建立conda环境，环境中软件的安装和卸载
查看环境

conda info --envs
# conda environments:
#
base                  *  /root/miniconda3

建立一个叫rnaseq的conda环境，然后指定python版本是3，安装软件fastqc、trimmomatic

conda create -n rna-seq python=3 fastqc trimmomatic -ycdca

再次查看环境

 conda info --envs
# conda environments:
#
base                  *  /root/miniconda3
rna-seq                  /root/miniconda3/envs/rna-seq

激活新的conda环境

source activate rna-seq

改变

image.png

输入fastqc看一看

fastqc
Exception in thread "main" java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
        at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:204)
        at java.awt.Window.<init>(Window.java:536)
        at java.awt.Frame.<init>(Frame.java:420)
        at java.awt.Frame.<init>(Frame.java:385)
        at javax.swing.JFrame.<init>(JFrame.java:189)
        at uk.ac.babraham.FastQC.FastQCApplication.<init>(FastQCApplication.java:63)
        at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:332)

卸载一个环境中的软件

conda remove -n rna-seq fastqc -y

卸载一个环境中全部软件

conda remove -n rna-seq -all
usage: conda [-h] [-V] command ...
conda: error: unrecognized arguments: -all

出错了，不知道为什么？是因为就剩一个软件了吗

结束啦，开心