Day3-李泽平-Linux环境下的软件安装
原创Day3-李泽平-Linux环境下的软件安装
原创
用户11040033
修改于 2024-03-25 00:19:11
修改于 2024-03-25 00:19:11
Linux环境下的软件安装
一、conda认识和下载
1、conda认识
conda=Linux的应用商店
minicoda=conda精华版=Linux的应用商店
2、将miniconda下载到服务器
（1）浏览器搜索“miniconda 清华”
（2）进入清华大学开源软件镜像站
（3）将miniconda下载到服务器
目的：安装64位最新版本（Miniconda3-py39_24.1.2-0-Linux-x86_64.sh）
①通过右键复制最新版本的下载链接(https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-py39_24.1.2-0-Linux-x86_64.sh)
②登录服务器（方法见Day2），进入biosoft目录（输入 cd biosft）
Last login: Sat Mar 23 23:49:05 2024 from 218.249.94.220
bio08@ecm-cefa:~$ cd biosoft③使用wget命令（输入wget 刚才复制的下载链接）
bio08@ecm-cefa:~/biosoft$ wget https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-py39_24.1.2-0-Linux-x86_64.sh3、安装miniconda
运行：bash Miniconda3-py39_24.1.2-0-Linux-x86_64.sh
bio08@ecm-cefa:~/biosoft$ bash Miniconda3-py39_24.1.2-0-Linux-x86_64.sh出现如下界面
bio08@ecm-cefa:~/biosoft$ bash Miniconda3-py39_24.1.2-0-Linux-x86_64.sh
Welcome to Miniconda3 py39_24.1.2-0
In order to continue the installation process, please review the license
agreement.
Please, press ENTER to continue
>>> q #输入q，跳过版权信息
END USER LICENSE AGREEMENT
This Anaconda End User License Agreement ("EULA") is between Anaconda, Inc., ("Anaconda"), and you ("You" or
"Customer"), the individual or entity acquiring and/or providing access to the Anaconda On-Premise Products. The EULA
governs your on-premise access to and use of Anaconda's downloadable Python and R distribution of conda, conda-build,
Python, and over 200 open-source scientific packages and dependencies ("Anaconda Distribution"); Anaconda's data science
and machine learning platform (the "Platform"); and Anaconda's related Software, Documentation, Content, and other
related desktop services, including APIs, through which any of the foregoing are provided to You (collectively, the
"On-Premise Products"). Capitalized terms used in these EULA and not otherwise defined herein are defined at
https://legal.anaconda.com/policies/en/?name=anaconda-legal-definitions.
AS SET FORTH IN SECTION 1 BELOW, THERE ARE VARIOUS TYPES OF USERS FOR THE ON-PREMISE PRODUCTS, THUS, EXCEPT WHERE
INDICATED OTHERWISE "YOU" SHALL REFER TO CUSTOMER AND ALL TYPES OF USERS. YOU ACKNOWLEDGE THAT THIS EULA IS BINDING, AND
YOU AFFIRM AND SIGNIFY YOUR CONSENT TO THIS EULA, BY : (I) CLICKING A BUTTON OR CHECKBOX, (II) SIGNING A SIGNATURE BLOCK
SIGNIFYING YOUR ACCEPTANCE OF THIS EULA; AND/OR (III) REGISTERING TO, USING, OR ACCESSING THE ON-PREMISE PRODUCTS,
WHICHEVER IS EARLIER (THE "EFFECTIVE DATE").
Except as may be expressly permitted by this EULA, You may not sell or exchange anything You copy or derive from our
On-Premise Products. Subject to your compliance with this EULA, Anaconda grants You a personal, non-exclusive,
non-transferable, limited right to use our On-Premise Products strictly as detailed herein.
1. PLANS & ACCOUNTS
1.1 OUR PLANS. Unless otherwise provided in an applicable Order or Documentation, access to the On-Premise Products is
offered on a Subscription basis, and the features and limits of your access are determined by the subscribed plan or
tier ("Plan") You select, register for, purchase, renew, or upgrade or downgrade into. To review the features and price
associated with the Plans, please visit https://www.anaconda.com/pricing. Additional Offering Specific Terms may apply
to You, the Plan, or the On-Premise Product, and such specific terms are incorporated herein by reference and form an
integral part hereof.
a. FREE PLANS. Anaconda allows You to use the Free Offerings (as defined hereinafter), Trial Offerings (as defined
hereinafter), Pre-Release Offerings (as defined hereinafter), and Scholarships (as defined hereinafter) (each, a "Free
Plan"), without charge, as set forth in this Section 1.1(a). Your use of the Free Plan is restricted to Internal
Business Purposes. If You receive a Free Plan to the On-Premise Products, Anaconda grants You a non-transferable,
non-exclusive, revocable, limited license to use and access the On-Premise Products in strict accordance with this EULA.
We reserve the right, in our absolute discretion, to withdraw or to modify your Free Plan access to the On-Premise
Do you accept the license terms? [yes|no]
>>> yes #输入yes，按回车
Miniconda3 will now be installed into this location:
/home/bio08/miniconda3
- Press ENTER to confirm the location
- Press CTRL-C to abort the installation
- Or specify a different location below
[/home/bio08/miniconda3] >>> #按enter键确认安装地址
PREFIX=/home/bio08/miniconda3
Unpacking payload ...
Installing base environment...
Downloading and Extracting Packages:
Downloading and Extracting Packages:
Preparing transaction: done
Executing transaction: done
installation finished.
Do you wish to update your shell profile to automatically initialize conda?
This will activate conda on startup and change the command prompt when activated.
If you'd prefer that conda's base environment not be activated on startup,
run the following command when conda is activated:
conda config --set auto_activate_base false
You can undo this by running `conda init --reverse $SHELL`? [yes|no]
[no] >>> yes #输入yes并回车
no change /home/bio08/miniconda3/condabin/conda
no change /home/bio08/miniconda3/bin/conda
no change /home/bio08/miniconda3/bin/conda-env
no change /home/bio08/miniconda3/bin/activate
no change /home/bio08/miniconda3/bin/deactivate
no change /home/bio08/miniconda3/etc/profile.d/conda.sh
no change /home/bio08/miniconda3/etc/fish/conf.d/conda.fish
no change /home/bio08/miniconda3/shell/condabin/Conda.psm1
no change /home/bio08/miniconda3/shell/condabin/conda-hook.ps1
no change /home/bio08/miniconda3/lib/python3.9/site-packages/xontrib/conda.xsh
no change /home/bio08/miniconda3/etc/profile.d/conda.csh
modified /home/bio08/.bashrc
==> For changes to take effect, close and re-open your current shell. <==
Thank you for installing Miniconda3! #安装成功
bio08@ecm-cefa:~/biosoft$ 4、激活
输入source ~/.bashrc，注意空格
接着在命令行输入conda，出现满屏的信息说明成功了。
bio08@ecm-cefa:~/biosoft$ source ~/.bashrc # 输入source ~/.bashrc
(base) bio08@ecm-cefa:~/biosoft$ conda #输入conda
usage: conda [-h] [-v] [--no-plugins] [-V] COMMAND ...
conda is a tool for managing and deploying applications, environments and packages.
optional arguments:
-h, --help Show this help message and exit.
-v, --verbose Can be used multiple times. Once for detailed output, twice for INFO logging, thrice for DEBUG logging, four
times for TRACE logging.
--no-plugins Disable all plugins that are not built into conda.
-V, --version Show the conda version number and exit.
commands:
The following built-in and plugins subcommands are available.
COMMAND
activate Activate a conda environment.
clean Remove unused packages and caches.
compare Compare packages between conda environments.
config Modify configuration values in .condarc.
content-trust Signing and verification tools for Conda
create Create a new conda environment from a list of specified packages.
deactivate Deactivate the current active conda environment.
doctor Display a health report for your environment.
info Display information about current conda install.
init Initialize conda for shell interaction.
install Install a list of packages into a specified conda environment.
list List installed packages in a conda environment.
notices Retrieve latest channel notifications.
package Create low-level conda packages. (EXPERIMENTAL)
remove (uninstall)
Remove a list of packages from a specified conda environment.
rename Rename an existing environment.
repoquery Advanced search for repodata.
run Run an executable in a conda environment.
search Search for packages and display associated information using the MatchSpec format.
update (upgrade) Update conda packages to the latest compatible version.
(base) bio08@ecm-cefa:~/biosoft$ 5、添加镜像
镜像网站相当于主网站的副本，conda在国外，在国内下载软件速度慢，从镜像网站下载，可以加快下载速度
#使用北外的镜像，在命令行输入一下代码。
conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda/
conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/
conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/free/
conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/main/
conda config --set show_channel_urls yes
(base) bio08@ecm-cefa:~/biosoft$ conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda/
(base) bio08@ecm-cefa:~/biosoft$ conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/
(base) bio08@ecm-cefa:~/biosoft$ conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/free/
(base) bio08@ecm-cefa:~/biosoft$ conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/main/
(base) bio08@ecm-cefa:~/biosoft$ conda config --set show_channel_urls yes
(base) bio08@ecm-cefa:~/biosoft$ ***
二、使用conda
1、查看当前服务器上安装的所有软件列表
输入conda list
(base) bio08@ecm-cefa:~/biosoft$ conda list
# packages in environment at /home/bio08/miniconda3:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main defaults
_openmp_mutex 5.1 1_gnu defaults
archspec 0.2.1 pyhd3eb1b0_0 defaults
boltons 23.0.0 py39h06a4308_0 defaults
brotli-python 1.0.9 py39h6a678d5_7 defaults
bzip2 1.0.8 h7b6447c_0 defaults
c-ares 1.19.1 h5eee18b_0 defaults
ca-certificates 2023.12.12 h06a4308_0 defaults
certifi 2024.2.2 py39h06a4308_0 defaults
cffi 1.16.0 py39h5eee18b_0 defaults
charset-normalizer 2.0.4 pyhd3eb1b0_0 defaults
conda 24.1.2 py39h06a4308_0 defaults
conda-content-trust 0.2.0 py39h06a4308_0 defaults
conda-libmamba-solver 24.1.0 pyhd3eb1b0_0 defaults
conda-package-handling 2.2.0 py39h06a4308_0 defaults
conda-package-streaming 0.9.0 py39h06a4308_0 defaults
cryptography 42.0.2 py39hdda0065_0 defaults
distro 1.8.0 py39h06a4308_0 defaults
fmt 9.1.0 hdb19cb5_0 defaults
icu 73.1 h6a678d5_0 defaults
idna 3.4 py39h06a4308_0 defaults
jsonpatch 1.32 pyhd3eb1b0_0 defaults
jsonpointer 2.1 pyhd3eb1b0_0 defaults
krb5 1.20.1 h143b758_1 defaults
ld_impl_linux-64 2.38 h1181459_1 defaults
libarchive 3.6.2 h6ac8c49_2 defaults
libcurl 8.5.0 h251f7ec_0 defaults
libedit 3.1.20230828 h5eee18b_0 defaults
libev 4.33 h7f8727e_1 defaults
libffi 3.4.4 h6a678d5_0 defaults
libgcc-ng 11.2.0 h1234567_1 defaults
libgomp 11.2.0 h1234567_1 defaults
libmamba 1.5.6 haf1ee3a_0 defaults
libmambapy 1.5.6 py39h2dafd23_0 defaults
libnghttp2 1.57.0 h2d74bed_0 defaults
libsolv 0.7.24 he621ea3_0 defaults
libssh2 1.10.0 hdbd6064_2 defaults
libstdcxx-ng 11.2.0 h1234567_1 defaults
libxml2 2.10.4 hf1b16e4_1 defaults
lz4-c 1.9.4 h6a678d5_0 defaults
menuinst 2.0.2 py39h06a4308_0 defaults
ncurses 6.4 h6a678d5_0 defaults
openssl 3.0.13 h7f8727e_0 defaults
packaging 23.1 py39h06a4308_0 defaults
pcre2 10.42 hebb0a14_0 defaults
pip 23.3.1 py39h06a4308_0 defaults
platformdirs 3.10.0 py39h06a4308_0 defaults
pluggy 1.0.0 py39h06a4308_1 defaults
pybind11-abi 4 hd3eb1b0_1 defaults
pycosat 0.6.6 py39h5eee18b_0 defaults
pycparser 2.21 pyhd3eb1b0_0 defaults
pysocks 1.7.1 py39h06a4308_0 defaults
python 3.9.18 h955ad1f_0 defaults
readline 8.2 h5eee18b_0 defaults
reproc 14.2.4 h295c915_1 defaults
reproc-cpp 14.2.4 h295c915_1 defaults
requests 2.31.0 py39h06a4308_1 defaults
ruamel.yaml 0.17.21 py39h5eee18b_0 defaults
ruamel.yaml.clib 0.2.6 py39h5eee18b_1 defaults
setuptools 68.2.2 py39h06a4308_0 defaults
sqlite 3.41.2 h5eee18b_0 defaults
tk 8.6.12 h1ccaba5_0 defaults
tqdm 4.65.0 py39hb070fc8_0 defaults
tzdata 2023d h04d1e81_0 defaults
urllib3 2.1.0 py39h06a4308_1 defaults
wheel 0.41.2 py39h06a4308_0 defaults
xz 5.4.5 h5eee18b_0 defaults
yaml-cpp 0.8.0 h6a678d5_0 defaults
zlib 1.2.13 h5eee18b_0 defaults
zstandard 0.19.0 py39h5eee18b_0 defaults
zstd 1.5.5 hc292b87_0 defaults
(base) bio08@ecm-cefa:~/biosoft$ 2、安装软件fastqc
输入conda install fastqc -y，其中-y是yes，安装过程中conda问你的问题全部回答yes
(base) bio08@ecm-cefa:~/biosoft$ conda install fastqc -y #输入conda install fastqc -y
Channels:
- https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
- https://mirrors.bfsu.edu.cn/anaconda/pkgs/free
- https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge
- https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda
- defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /home/bio08/miniconda3
added / updated specs:
- fastqc
The following packages will be downloaded:
package | build
---------------------------|-----------------
archspec-0.2.3 | pyhd3eb1b0_0 47 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
ca-certificates-2024.3.11 | h06a4308_0 127 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
conda-24.3.0 | py39h06a4308_0 946 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
dbus-1.13.18 | hb2f20db_0 504 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
expat-2.5.0 | h6a678d5_0 172 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
fastqc-0.12.1 | hdfd78af_0 11.1 MB https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda
font-ttf-dejavu-sans-mono-2.37| hd3eb1b0_0 335 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
fontconfig-2.14.1 | h4c34cd2_2 281 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
freetype-2.12.1 | h4a9f257_0 626 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
gdbm-1.18 | hd4cb3f1_4 194 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
glib-2.78.4 | h6a678d5_0 508 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
glib-tools-2.78.4 | h6a678d5_0 115 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libglib-2.78.4 | hdc74915_0 1.5 MB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libiconv-1.16 | h7f8727e_2 736 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libpng-1.6.39 | h5eee18b_0 304 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libuuid-1.41.5 | h5eee18b_0 27 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
libxcb-1.15 | h7f8727e_0 505 KB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
openjdk-11.0.13 | h87a67e3_0 341.0 MB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
perl-5.34.0 | h5eee18b_2 12.4 MB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
------------------------------------------------------------
Total: 371.3 MB
The following NEW packages will be INSTALLED:
dbus anaconda/pkgs/main/linux-64::dbus-1.13.18-hb2f20db_0
expat anaconda/pkgs/main/linux-64::expat-2.5.0-h6a678d5_0
fastqc anaconda/cloud/bioconda/noarch::fastqc-0.12.1-hdfd78af_0
font-ttf-dejavu-s~ anaconda/pkgs/main/noarch::font-ttf-dejavu-sans-mono-2.37-hd3eb1b0_0
fontconfig anaconda/pkgs/main/linux-64::fontconfig-2.14.1-h4c34cd2_2
freetype anaconda/pkgs/main/linux-64::freetype-2.12.1-h4a9f257_0
gdbm anaconda/pkgs/main/linux-64::gdbm-1.18-hd4cb3f1_4
glib anaconda/pkgs/main/linux-64::glib-2.78.4-h6a678d5_0
glib-tools anaconda/pkgs/main/linux-64::glib-tools-2.78.4-h6a678d5_0
libglib anaconda/pkgs/main/linux-64::libglib-2.78.4-hdc74915_0
libiconv anaconda/pkgs/main/linux-64::libiconv-1.16-h7f8727e_2
libpng anaconda/pkgs/main/linux-64::libpng-1.6.39-h5eee18b_0
libuuid anaconda/pkgs/main/linux-64::libuuid-1.41.5-h5eee18b_0
libxcb anaconda/pkgs/main/linux-64::libxcb-1.15-h7f8727e_0
openjdk anaconda/pkgs/main/linux-64::openjdk-11.0.13-h87a67e3_0
perl anaconda/pkgs/main/linux-64::perl-5.34.0-h5eee18b_2
The following packages will be UPDATED:
archspec pkgs/main::archspec-0.2.1-pyhd3eb1b0_0 --> anaconda/pkgs/main::archspec-0.2.3-pyhd3eb1b0_0
ca-certificates pkgs/main::ca-certificates-2023.12.12~ --> anaconda/pkgs/main::ca-certificates-2024.3.11-h06a4308_0
conda pkgs/main::conda-24.1.2-py39h06a4308_0 --> anaconda/pkgs/main::conda-24.3.0-py39h06a4308_0
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(base) bio08@ecm-cefa:~/biosoft$ 3、确认fastqc是否安装成功
输入fastqc --help，如果出现一大片文字，这是软件的帮助文档。因为只有安装成功的软件才能看到帮助文档，所以出现了这篇帮助文档，就可以确定已经安装成功。
(base) bio08@ecm-cefa:~/biosoft$ fastqc --help ***
三、小结（思维导图）
***
四、参考资料
微信公众号生信星球
原创声明：本文系作者授权腾讯云开发者社区发表，未经许可，不得转载。
如有侵权，请联系 cloudcommunity@tencent.com 删除。
原创声明：本文系作者授权腾讯云开发者社区发表，未经许可，不得转载。
如有侵权，请联系 cloudcommunity@tencent.com 删除。
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