生信星球Day3-杨羽茜

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
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