linux环境下的软件安装
1. 下载miniconda
miniconda
1.1查看服务器
bio08@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
1.2下载成功
bio08@VM-0-6-ubuntu:~/biosoft$ wget https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-latest-Linux-x86_64.sh
--2021-04-21 21:19:29-- https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-latest-Linux-x86_64.sh
Resolving mirrors.tuna.tsinghua.edu.cn (mirrors.tuna.tsinghua.edu.cn)... 101.6.8.193, 2402:f000:1:408:8100::1
Connecting to mirrors.tuna.tsinghua.edu.cn (mirrors.tuna.tsinghua.edu.cn)|101.6.8.193|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 94235922 (90M) [application/octet-stream]
Saving to: ‘Miniconda3-latest-Linux-x86_64.sh’
Miniconda3-latest-Linux-x86_64.sh 100%[====================================================================>] 89.87M 12.2MB/s in 12s
2021-04-21 21:19:42 (7.27 MB/s) - ‘Miniconda3-latest-Linux-x86_64.sh’ saved [94235922/94235922]
2.安装miniconda
bio08@VM-0-6-ubuntu:~/biosoft$ bash Miniconda3-latest-Linux-x86_64.sh
安装
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!
激活
bio08@VM-0-6-ubuntu:~/biosoft$ source ~/.bashrc
成功
(base) bio08@VM-0-6-ubuntu:~/biosoft$ conda
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/bio08/.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
添加镜像
(base) bio08@VM-0-6-ubuntu:~/biosoft$ conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
bioconda
conda config --set show_channel_urls yes(base) bio08@VM-0-6-ubuntu:~/biosoft$ conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
(base) bio08@VM-0-6-ubuntu:~/biosoft$ conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
(base) bio08@VM-0-6-ubuntu:~/biosoft$ conda config --set show_channel_urls yes
3.使用conda
3.1查看当前服务器上安装的所有软件列表
(base) bio08@VM-0-6-ubuntu:~$ conda list
# packages in environment at /home/bio08/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
conda 4.9.2 py38h06a4308_0 defaults
conda-package-handling 1.7.2 py38h03888b9_0 defaults
cryptography 3.2.1 py38h3c74f83_1 defaults
idna 2.10 py_0 defaults
ld_impl_linux-64 2.33.1 h53a641e_7 defaults
libedit 3.1.20191231 h14c3975_1 defaults
libffi 3.3 he6710b0_2 defaults
libgcc-ng 9.1.0 hdf63c60_0 defaults
libstdcxx-ng 9.1.0 hdf63c60_0 defaults
ncurses 6.2 he6710b0_1 defaults
openssl 1.1.1h h7b6447c_0 defaults
pip 20.2.4 py38h06a4308_0 defaults
pycosat 0.6.3 py38h7b6447c_1 defaults
pycparser 2.20 py_2 defaults
pyopenssl 19.1.0 pyhd3eb1b0_1 defaults
pysocks 1.7.1 py38h06a4308_0 defaults
python 3.8.5 h7579374_1 defaults
readline 8.0 h7b6447c_0 defaults
requests 2.24.0 py_0 defaults
ruamel_yaml 0.15.87 py38h7b6447c_1 defaults
setuptools 50.3.1 py38h06a4308_1 defaults
six 1.15.0 py38h06a4308_0 defaults
sqlite 3.33.0 h62c20be_0 defaults
tk 8.6.10 hbc83047_0 defaults
tqdm 4.51.0 pyhd3eb1b0_0 defaults
urllib3 1.25.11 py_0 defaults
wheel 0.35.1 pyhd3eb1b0_0 defaults
xz 5.2.5 h7b6447c_0 defaults
yaml 0.2.5 h7b6447c_0 defaults
zlib 1.2.11 h7b6447c_3 defaults
3.2安装软件
(base) bio08@VM-0-6-ubuntu:~$ conda install fastqc -y
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.9.2
latest version: 4.10.1
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/bio08/miniconda3
added / updated specs:
- fastqc
The following packages will be downloaded:
package | build
3.3删除软件
(base) bio08@VM-0-6-ubuntu:~$ conda remove fastqc -y
Collecting package metadata (repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /home/bio08/miniconda3
removed specs:
- fastqc
