2020年9月9日 杨羽茜
Miniconda的安装
查找下载链接
百度/谷歌搜索“miniconda 清华”（是清华的conda镜像网站）
https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/
明确服务器系统版本
uname -a
明确下载版本及下载链接，复制下载链接
「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
服务器中miniconda下载
##安装miniconda
```bash Miniconda3-latest-Linux-x86_64.sh
```bio04@VM-0-10-ubuntu:~/biosoft$ bash Miniconda3-latest-Linux-x86_64.sh
Welcome to Miniconda3 4.7.12
In order to continue the installation process, please review the license
agreement.
Please, press ENTER to continue
>>>
===================================
Miniconda End User License Agreement
===================================
Copyright 2015, Anaconda, Inc.
All rights reserved under the 3-clause BSD License:
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice, th
is list of conditions and the following disclaimer in the documentation and/or o
ther materials provided with the distribution.
* Neither the name of Anaconda, Inc. ("Anaconda, Inc.") nor the names of its c
ontributors may be used to endorse or promote products derived from this softwar
e without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WA
RRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL ANACONDA, INC. BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL
, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, P
ROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BU
SINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN C
ONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING I
N ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
SUCH DAMAGE.
Notice of Third Party Software Licenses
=======================================
Miniconda contains open source software packages from third parties. These are a
vailable on an "as is" basis and subject to their individual license agreements.
These licenses are available in Anaconda Distribution or at http://docs.anacond
a.com/anaconda/pkg-docs. Any binary packages of these third party tools you obta
in via Anaconda Distribution are subject to their individual licenses as well as
the Anaconda license. Anaconda, Inc. reserves the right to change which third p
arty tools are provided in Miniconda.
Cryptography Notice
===================
This distribution includes cryptographic software. The country in which you curr
ently reside may have restrictions on the import, possession, use, and/or re-exp
ort to another country, of encryption software. BEFORE using any encryption soft
ware, please check your country's laws, regulations and policies concerning the
import, possession, or use, and re-export of encryption software, to see if this
is permitted. See the Wassenaar Arrangement http://www.wassenaar.org/ for more
information.
Anaconda, Inc. has self-classified this software as Export Commodity Control Num
ber (ECCN) 5D992b, which includes mass market information security software usin
g or performing cryptographic functions with asymmetric algorithms. No license i
s required for export of this software to non-embargoed countries. In addition,
the Intel(TM) Math Kernel Library contained in Anaconda, Inc.'s software is clas
sified by Intel(TM) as ECCN 5D992b with no license required for export to non-em
bargoed countries.
The following packages are included in this distribution that relate to cryptogr
aphy:
openssl
The OpenSSL Project is a collaborative effort to develop a robust, commercia
l-grade, full-featured, and Open Source toolkit implementing the Transport Layer
Security (TLS) and Secure Sockets Layer (SSL) protocols as well as a full-stren
gth general purpose cryptography library.
pycrypto
A collection of both secure hash functions (such as SHA256 and RIPEMD160), a
nd various encryption algorithms (AES, DES, RSA, ElGamal, etc.).
pyopenssl
A thin Python wrapper around (a subset of) the OpenSSL library.
kerberos (krb5, non-Windows platforms)
A network authentication protocol designed to provide strong authentication
for client/server applications by using secret-key cryptography.
cryptography
A Python library which exposes cryptographic recipes and primitives.
Do you accept the license terms? [yes|no]
[no] >>>
Please answer 'yes' or 'no':'
>>>
Please answer 'yes' or 'no':'
>>>
Please answer 'yes' or 'no':'
>>>
Please answer 'yes' or 'no':'
>>>
Please answer 'yes' or 'no':'
>>> yes
Miniconda3 will now be installed into this location:
/home/bio04/miniconda3
- Press ENTER to confirm the location
- Press CTRL-C to abort the installation
- Or specify a different location below
[/home/bio04/miniconda3] >>>
PREFIX=/home/bio04/miniconda3
Unpacking payload ...
Extracting : libedit-3.1.20181209-hc058e9b_0.conda: 3%| | 1/35 [00:00<00:01, 1Extracting : libgcc-ng-9.1.0-hdf63c60_0.conda: 6%| | 2/35 [00:00<00:02, 11.06iExtracting : libgcc-ng-9.1.0-hdf63c60_0.conda: 9%| | 3/35 [00:00<00:01, 16.57iExtracting : urllib3-1.24.2-py37_0.conda: 9%|▏ | 3/35 [00:00<00:01, 16.57it/s]Extracting : pyopenssl-19.0.0-py37_0.conda: 11%| | 4/35 [00:00<00:01, 16.57it/sExtracting : six-1.12.0-py37_0.conda: 14%|▊ | 5/35 [00:00<00:01, 16.57it/s]Extracting : libstdcxx-ng-9.1.0-hdf63c60_0.conda: 20%|▏| 7/35 [00:00<00:01, 16.Extracting : libstdcxx-ng-9.1.0-hdf63c60_0.conda: 23%|▏| 8/35 [00:00<00:01, 19.Extracting : python-3.7.4-h265db76_1.conda: 23%|▏| 8/35 [00:00<00:01, 19.98it/sExtracting : libffi-3.2.1-hd88cf55_4.conda: 26%|▎| 9/35 [00:00<00:01, 19.98it/sExtracting : libffi-3.2.1-hd88cf55_4.conda: 29%|▎| 10/35 [00:00<00:02, 8.45it/Extracting : pycparser-2.19-py37_0.conda: 29%|▎| 10/35 [00:00<00:02, 8.45it/s]Extracting : chardet-3.0.4-py37_1003.conda: 31%|▎| 11/35 [00:00<00:02, 8.45it/Extracting : readline-7.0-h7b6447c_5.conda: 34%|▎| 12/35 [00:00<00:02, 8.45it/Extracting : readline-7.0-h7b6447c_5.conda: 37%|▎| 13/35 [00:00<00:02, 10.47it/Extracting : yaml-0.1.7-had09818_2.conda: 37%|▎| 13/35 [00:01<00:02, 10.47it/s]Extracting : conda-package-handling-1.6.0-py37h7b6447c_0.conda: 40%|▍| 14/35 [0Extracting : pycosat-0.6.3-py37h14c3975_0.conda: 43%|▍| 15/35 [00:01<00:01, 10.Extracting : tk-8.6.8-hbc83047_0.conda: 46%|█▎ | 16/35 [00:01<00:01, 10.47it/s]Extracting : _libgcc_mutex-0.1-main.conda: 49%|▍| 17/35 [00:01<00:01, 12.61it/sExtracting : ncurses-6.1-he6710b0_1.conda: 51%|▌| 18/35 [00:01<00:01, 12.61it/sExtracting : ncurses-6.1-he6710b0_1.conda: 54%|▌| 19/35 [00:01<00:01, 12.16it/sExtracting : xz-5.2.4-h14c3975_4.conda: 54%|█▋ | 19/35 [00:01<00:01, 12.16it/s]Extracting : ruamel_yaml-0.15.46-py37h14c3975_0.conda: 57%|▌| 20/35 [00:01<00:0Extracting : tqdm-4.36.1-py_0.conda: 60%|███▌ | 21/35 [00:01<00:01, 12.16it/s]Extracting : certifi-2019.9.11-py37_0.tar.bz2: 66%|▋| 23/35 [00:01<00:00, 12.16Extracting : asn1crypto-1.2.0-py37_0.tar.bz2: 69%|▋| 24/35 [00:01<00:00, 12.16iExtracting : asn1crypto-1.2.0-py37_0.tar.bz2: 71%|▋| 25/35 [00:01<00:00, 15.42iExtracting : openssl-1.1.1d-h7b6447c_3.tar.bz2: 71%|▋| 25/35 [00:02<00:00, 15.4Extracting : cffi-1.13.0-py37h2e261b9_0.tar.bz2: 74%|▋| 26/35 [00:02<00:00, 15.Extracting : pip-19.3.1-py37_0.tar.bz2: 77%|██▎| 27/35 [00:02<00:00, 15.42it/s]Extracting : pysocks-1.7.1-py37_0.tar.bz2: 80%|▊| 28/35 [00:02<00:01, 6.11it/sExtracting : setuptools-41.4.0-py37_0.tar.bz2: 83%|▊| 29/35 [00:02<00:00, 6.11Extracting : setuptools-41.4.0-py37_0.tar.bz2: 86%|▊| 30/35 [00:02<00:00, 6.89Extracting : ca-certificates-2019.10.16-0.tar.bz2: 86%|▊| 30/35 [00:02<00:00, Extracting : conda-4.7.12-py37_0.tar.bz2: 89%|▉| 31/35 [00:03<00:00, 6.89it/s]Extracting : cryptography-2.8-py37h1ba5d50_0.tar.bz2: 94%|▉| 33/35 [00:03<00:00Extracting : cryptography-2.8-py37h1ba5d50_0.tar.bz2: 97%|▉| 34/35 [00:03<00:00Extracting : sqlite-3.30.0-h7b6447c_0.tar.bz2: 97%|▉| 34/35 [00:04<00:00, 6.04 Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /home/bio04/miniconda3
added / updated specs:
- _libgcc_mutex==0.1=main
- asn1crypto==1.2.0=py37_0
- ca-certificates==2019.10.16=0
- certifi==2019.9.11=py37_0
- cffi==1.13.0=py37h2e261b9_0
- chardet==3.0.4=py37_1003
- conda-package-handling==1.6.0=py37h7b6447c_0
- conda==4.7.12=py37_0
- cryptography==2.8=py37h1ba5d50_0
- idna==2.8=py37_0
- libedit==3.1.20181209=hc058e9b_0
- libffi==3.2.1=hd88cf55_4
- libgcc-ng==9.1.0=hdf63c60_0
- libstdcxx-ng==9.1.0=hdf63c60_0
- ncurses==6.1=he6710b0_1
- openssl==1.1.1d=h7b6447c_3
- pip==19.3.1=py37_0
- pycosat==0.6.3=py37h14c3975_0
- pycparser==2.19=py37_0
- pyopenssl==19.0.0=py37_0
- pysocks==1.7.1=py37_0
- python==3.7.4=h265db76_1
- readline==7.0=h7b6447c_5
- requests==2.22.0=py37_0
- ruamel_yaml==0.15.46=py37h14c3975_0
- setuptools==41.4.0=py37_0
- six==1.12.0=py37_0
- sqlite==3.30.0=h7b6447c_0
- tk==8.6.8=hbc83047_0
- tqdm==4.36.1=py_0
- urllib3==1.24.2=py37_0
- wheel==0.33.6=py37_0
- xz==5.2.4=h14c3975_4
- yaml==0.1.7=had09818_2
- zlib==1.2.11=h7b6447c_3
The following NEW packages will be INSTALLED:
_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
asn1crypto pkgs/main/linux-64::asn1crypto-1.2.0-py37_0
ca-certificates pkgs/main/linux-64::ca-certificates-2019.10.16-0
certifi pkgs/main/linux-64::certifi-2019.9.11-py37_0
cffi pkgs/main/linux-64::cffi-1.13.0-py37h2e261b9_0
chardet pkgs/main/linux-64::chardet-3.0.4-py37_1003
conda pkgs/main/linux-64::conda-4.7.12-py37_0
conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.0-py37h7b6447c_0
cryptography pkgs/main/linux-64::cryptography-2.8-py37h1ba5d50_0
idna pkgs/main/linux-64::idna-2.8-py37_0
libedit pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
libffi pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4
libgcc-ng pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
ncurses pkgs/main/linux-64::ncurses-6.1-he6710b0_1
openssl pkgs/main/linux-64::openssl-1.1.1d-h7b6447c_3
pip pkgs/main/linux-64::pip-19.3.1-py37_0
pycosat pkgs/main/linux-64::pycosat-0.6.3-py37h14c3975_0
pycparser pkgs/main/linux-64::pycparser-2.19-py37_0
pyopenssl pkgs/main/linux-64::pyopenssl-19.0.0-py37_0
pysocks pkgs/main/linux-64::pysocks-1.7.1-py37_0
python pkgs/main/linux-64::python-3.7.4-h265db76_1
readline pkgs/main/linux-64::readline-7.0-h7b6447c_5
requests pkgs/main/linux-64::requests-2.22.0-py37_0
ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.46-py37h14c3975_0
setuptools pkgs/main/linux-64::setuptools-41.4.0-py37_0
six pkgs/main/linux-64::six-1.12.0-py37_0
sqlite pkgs/main/linux-64::sqlite-3.30.0-h7b6447c_0
tk pkgs/main/linux-64::tk-8.6.8-hbc83047_0
tqdm pkgs/main/noarch::tqdm-4.36.1-py_0
urllib3 pkgs/main/linux-64::urllib3-1.24.2-py37_0
wheel pkgs/main/linux-64::wheel-0.33.6-py37_0
xz pkgs/main/linux-64::xz-5.2.4-h14c3975_4
yaml pkgs/main/linux-64::yaml-0.1.7-had09818_2
zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3
Preparing transaction: done
Executing transaction: done
installation finished.
Do you wish the installer to initialize Miniconda3
by running conda init? [yes|no]
[no] >>> no
You have chosen to not have conda modify your shell scripts at all.
To activate conda's base environment in your current shell session:
eval "$(/home/bio04/miniconda3/bin/conda shell.YOUR_SHELL_NAME hook)"
To install conda's shell functions for easier access, first activate, then:
conda init
If you'd prefer that conda's base environment not be activated on startup,
set the auto_activate_base parameter to false:
conda config --set auto_activate_base false
Thank you for installing Miniconda3!
##激活conda
```bio04@VM-0-10-ubuntu:~/biosoft$ source ~/.bashrc
(base) bio04@VM-0-10-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.
config Modify configuration values in .condarc. This is modeled
after the git config command. Writes to the user .condarc
file (/home/bio04/.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
```#使用清华镜像
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
# conda使用
##查看软件
conda list
##安装软件
conda install fastqc -y
#卸载软件
conda remove fastqc -y
