学习小组Day3笔记--xr
2020-09-16 本文已影响0人
xryyz
今天的学习内容是在Linux上安装软件，用miniconda进行fastqc的安装
1.miniconda安装
conda具备多款软件，大部分生物信息学分析软件可以用miniconda进行安装
1.1下载和安装miniconda
1.1.1确定miniconda的下载网址
搜索：miniconda 清华
找到miniconda的安装网址
https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/
用uname -a命令查看服务器的是多少位
打开服务安装软件的文件夹 cd biosoft
安装最新版本
wget https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
安装提示说按Enter键继续时就按Enter键
这步输入yes
这步可以输入no
输入yes是让conda自动给你配置环境变量
输入yes的结果是：~/.bashrc这里文件里最后几行多了conda的配置信息
1.2激活miniconda
source ~/.bashrc #激活
conda #命令行输入conda看能不能跑，如果出现以下信息就说明安装成功
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.
config Modify configuration values in .condarc. This is modeled after the git config command. Writes to the user .condarc file (/home/bio07/.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
如果没安装成功则删除miniconda这个目录
1.3添加镜像
conda是国外的，添加镜像才能从镜像网站下载，加快下载速度
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
conda config --set show_channel_urls yes
注：
之前忘记添加镜像
出现了如下报错
Do you wish the installer to initialize Miniconda3
by running conda init? [yes|no]
[no] >>> yes
no change /home/bio07/miniconda3/condabin/conda
no change /home/bio07/miniconda3/bin/conda
no change /home/bio07/miniconda3/bin/conda-env
no change /home/bio07/miniconda3/bin/activate
no change /home/bio07/miniconda3/bin/deactivate
no change /home/bio07/miniconda3/etc/profile.d/conda.sh
no change /home/bio07/miniconda3/etc/fish/conf.d/conda.fish
no change /home/bio07/miniconda3/shell/condabin/Conda.psm1
no change /home/bio07/miniconda3/shell/condabin/conda-hook.ps1
no change /home/bio07/miniconda3/lib/python3.8/site-packages/xontrib/conda.xsh
no change /home/bio07/miniconda3/etc/profile.d/conda.csh
no change /home/bio07/.bashrc
No action taken.
If you'd prefer that conda's base environment not be activated on startup,
set the auto_activate_base parameter to false:
conda config --set auto_activate_base false
Thank you for installing Miniconda3!
2.使用miniconda安装fastqc
2.1查看当前服务器上安装的所有软件列表
conda list #查看软件
# packages in environment at /home/bio07/miniconda3:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main defaults
ca-certificates 2020.1.1 0 defaults
certifi 2020.4.5.1 py38_0 defaults
cffi 1.14.0 py38he30daa8_1 defaults
chardet 3.0.4 py38_1003 defaults
conda 4.8.3 py38_0 defaults
conda-package-handling 1.6.1 py38h7b6447c_0 defaults
cryptography 2.9.2 py38h1ba5d50_0 defaults
idna 2.9 py_1 defaults
ld_impl_linux-64 2.33.1 h53a641e_7 defaults
libedit 3.1.20181209 hc058e9b_0 defaults
libffi 3.3 he6710b0_1 defaults
libgcc-ng 9.1.0 hdf63c60_0 defaults
libstdcxx-ng 9.1.0 hdf63c60_0 defaults
ncurses 6.2 he6710b0_1 defaults
openssl 1.1.1g h7b6447c_0 defaults
pip 20.0.2 py38_3 defaults
pycosat 0.6.3 py38h7b6447c_1 defaults
pycparser 2.20 py_0 defaults
pyopenssl 19.1.0 py38_0 defaults
pysocks 1.7.1 py38_0 defaults
python 3.8.3 hcff3b4d_0 defaults
readline 8.0 h7b6447c_0 defaults
requests 2.23.0 py38_0 defaults
ruamel_yaml 0.15.87 py38h7b6447c_0 defaults
setuptools 46.4.0 py38_0 defaults
six 1.14.0 py38_0 defaults
sqlite 3.31.1 h62c20be_1 defaults
tk 8.6.8 hbc83047_0 defaults
tqdm 4.46.0 py_0 defaults
urllib3 1.25.8 py38_0 defaults
wheel 0.34.2 py38_0 defaults
xz 5.2.5 h7b6447c_0 defaults
yaml 0.1.7 had09818_2 defaults
zlib 1.2.11 h7b6447c_3 defaults
2.2用coda搜索需要安装的软件
conda search fastqc #需要点时间
#出现以下结果
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 4 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 5 anaconda/cloud/bioconda
fastqc 0.11.7 6 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
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
2.3安装软件
conda install fastqc -y #-y是yes，安装过程中conda问你的问题全部自动回答yes
#出现以下结果
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.3
latest version: 4.8.4
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/bio07/miniconda3
added / updated specs:
- fastqc
The following packages will be downloaded:
package | build
---------------------------|-----------------
ca-certificates-2020.6.20 | hecda079_0 145 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
certifi-2020.6.20 | py38h32f6830_0 151 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
conda-4.8.5 | py38h32f6830_1 3.1 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fastqc-0.11.9 | 0 9.7 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
font-ttf-dejavu-sans-mono-2.37| hab24e00_0 388 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fontconfig-2.13.1 | h1056068_1002 365 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
freetype-2.10.2 | he06d7ca_0 905 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
icu-67.1 | he1b5a44_0 12.9 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libiconv-1.16 | h516909a_0 1.4 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libpng-1.6.37 | hed695b0_2 359 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libuuid-2.32.1 | h14c3975_1000 26 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libxml2-2.9.10 | h68273f3_2 1.3 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
openjdk-10.0.2 | h14c3975_1015 189.2 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
openssl-1.1.1g | h516909a_1 2.1 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
perl-5.30.3 | h516909a_1 16.4 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python_abi-3.8 | 1_cp38 4 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
------------------------------------------------------------
Total: 238.3 MB
The following NEW packages will be INSTALLED:
fastqc anaconda/cloud/bioconda/noarch::fastqc-0.11.9-0
font-ttf-dejavu-s~ anaconda/cloud/conda-forge/noarch::font-ttf-dejavu-sans-mono-2.37-hab24e00_0
fontconfig anaconda/cloud/conda-forge/linux-64::fontconfig-2.13.1-h1056068_1002
freetype anaconda/cloud/conda-forge/linux-64::freetype-2.10.2-he06d7ca_0
icu anaconda/cloud/conda-forge/linux-64::icu-67.1-he1b5a44_0
libiconv anaconda/cloud/conda-forge/linux-64::libiconv-1.16-h516909a_0
libpng anaconda/cloud/conda-forge/linux-64::libpng-1.6.37-hed695b0_2
libuuid anaconda/cloud/conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000
libxml2 anaconda/cloud/conda-forge/linux-64::libxml2-2.9.10-h68273f3_2
openjdk anaconda/cloud/conda-forge/linux-64::openjdk-10.0.2-h14c3975_1015
perl anaconda/cloud/conda-forge/linux-64::perl-5.30.3-h516909a_1
python_abi anaconda/cloud/conda-forge/linux-64::python_abi-3.8-1_cp38
The following packages will be UPDATED:
ca-certificates pkgs/main::ca-certificates-2020.1.1-0 --> anaconda/cloud/conda-forge::ca-certificates-2020.6.20-hecda079_0
certifi pkgs/main::certifi-2020.4.5.1-py38_0 --> anaconda/cloud/conda-forge::certifi-2020.6.20-py38h32f6830_0
conda pkgs/main::conda-4.8.3-py38_0 --> anaconda/cloud/conda-forge::conda-4.8.5-py38h32f6830_1
openssl pkgs/main::openssl-1.1.1g-h7b6447c_0 --> anaconda/cloud/conda-forge::openssl-1.1.1g-h516909a_1
Downloading and Extracting Packages
libuuid-2.32.1 | 26 KB | ############################################################################################################################ | 100%
libiconv-1.16 | 1.4 MB | ############################################################################################################################ | 100%
font-ttf-dejavu-sans | 388 KB | ############################################################################################################################ | 100%
certifi-2020.6.20 | 151 KB | ############################################################################################################################ | 100%
ca-certificates-2020 | 145 KB | ############################################################################################################################ | 100%
libxml2-2.9.10 | 1.3 MB | ############################################################################################################################ | 100%
libpng-1.6.37 | 359 KB | ############################################################################################################################ | 100%
fontconfig-2.13.1 | 365 KB | ############################################################################################################################ | 100%
freetype-2.10.2 | 905 KB | ############################################################################################################################ | 100%
python_abi-3.8 | 4 KB | ############################################################################################################################ | 100%
perl-5.30.3 | 16.4 MB | ############################################################################################################################ | 100%
fastqc-0.11.9 | 9.7 MB | ############################################################################################################################ | 100%
conda-4.8.5 | 3.1 MB | ############################################################################################################################ | 100%
openssl-1.1.1g | 2.1 MB | ############################################################################################################################ | 100%
icu-67.1 | 12.9 MB | ############################################################################################################################ | 100%
openjdk-10.0.2 | 189.2 MB | ############################################################################################################################ | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#安装完成
3.卸载fastqc
conda remove fastqc -y
