宏宏的学习笔记Day3 Linux环境下的软件安装
原创
1.wget命令
下载miniconda至服务器
(base) bio05@ecm-cefa:~/biosoft$ wget https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-latest-Linux-x86_64.sh
--2024-04-15 20:15:18-- 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)... 101.6.15.130, 2402:f000:1:400::2
Connecting to mirrors.tuna.tsinghua.edu.cn (mirrors.tuna.tsinghua.edu.cn)|101.6.15.130|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 144041912 (137M) [application/octet-stream]
Saving to: ‘Miniconda3-latest-Linux-x86_64.sh’
Miniconda3-latest-L 100%[===================>] 137.37M 3.02MB/s in 44s
2024-04-15 20:16:03 (3.09 MB/s) - ‘Miniconda3-latest-Linux-x86_64.sh’ saved [144041912/144041912]2.安装miniconda
(base) bio05@ecm-cefa:~/biosoft$ bash Miniconda3-latest-Linux-x86_64.sh
Welcome to Miniconda3 py312_24.1.2-0
In order to continue the installation process, please review the license
agreement.
Please, press ENTER to continue
>>>
END USER LICENSE AGREEMENT
This Anaconda End User License Agreement ("EULA") is between Anaconda, Inc., ("A
naconda"), and you ("You" or
"Customer"), the individual or entity acquiring and/or providing access to the A
naconda 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 d
efined 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-PRE
MISE PRODUCTS, THUS, EXCEPT WHERE
INDICATED OTHERWISE "YOU" SHALL REFER TO CUSTOMER AND ALL TYPES OF USERS. YOU AC
KNOWLEDGE THAT THIS EULA IS BINDING, AND
YOU AFFIRM AND SIGNIFY YOUR CONSENT TO THIS EULA, BY : (I) CLICKING A BUTTON OR
Do you accept the license terms? [yes|no]
>>> yes
Miniconda3 will now be installed into this location:
/home/bio05/miniconda3
- Press ENTER to confirm the location
- Press CTRL-C to abort the installation
- Or specify a different location below
[/home/bio05/miniconda3] >>>
PREFIX=/home/bio05/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 $SHELL`? [yes|no]
[no] >>> yes
no change /home/bio05/miniconda3/condabin/conda
no change /home/bio05/miniconda3/bin/conda
no change /home/bio05/miniconda3/bin/conda-env
no change /home/bio05/miniconda3/bin/activate
no change /home/bio05/miniconda3/bin/deactivate
no change /home/bio05/miniconda3/etc/profile.d/conda.sh
no change /home/bio05/miniconda3/etc/fish/conf.d/conda.fish
no change /home/bio05/miniconda3/shell/condabin/Conda.psm1
no change /home/bio05/miniconda3/shell/condabin/conda-hook.ps1
no change /home/bio05/miniconda3/lib/python3.12/site-packages/xontrib/conda.xsh
no change /home/bio05/miniconda3/etc/profile.d/conda.csh
no change /home/bio05/.bashrc
No action taken.
Thank you for installing Miniconda3!3.激活miniconda
source ~/.bashrc4.查看服务器上安装的所有软件列表
conda list
(base) bio05@ecm-cefa:~/biosoft$ conda list
# packages in environment at /home/bio05/miniconda3:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
archspec 0.2.1 pyhd3eb1b0_0
boltons 23.0.0 py312h06a4308_0
brotli-python 1.0.9 py312h6a678d5_7
bzip2 1.0.8 h7b6447c_0
c-ares 1.19.1 h5eee18b_0
ca-certificates 2023.12.12 h06a4308_0
certifi 2024.2.2 py312h06a4308_0
cffi 1.16.0 py312h5eee18b_0
charset-normalizer 2.0.4 pyhd3eb1b0_0
conda 24.1.2 py312h06a4308_0
conda-content-trust 0.2.0 py312h06a4308_0
conda-libmamba-solver 23.12.0 pyhd3eb1b0_1
conda-package-handling 2.2.0 py312h06a4308_0
conda-package-streaming 0.9.0 py312h06a4308_0
cryptography 41.0.7 py312hdda0065_0
distro 1.8.0 py312h06a4308_0
expat 2.5.0 h6a678d5_0
fmt 9.1.0 hdb19cb5_0
icu 73.1 h6a678d5_0
idna 3.4 py312h06a4308_0
jsonpatch 1.32 pyhd3eb1b0_0
jsonpointer 2.1 pyhd3eb1b0_0
krb5 1.20.1 h143b758_1
ld_impl_linux-64 2.38 h1181459_1
libarchive 3.6.2 h6ac8c49_2
libcurl 8.5.0 h251f7ec_0
libedit 3.1.20230828 h5eee18b_0
libev 4.33 h7f8727e_1
libffi 3.4.4 h6a678d5_0
libgcc-ng 11.2.0 h1234567_1
libgomp 11.2.0 h1234567_1
libmamba 1.5.3 haf1ee3a_0
libmambapy 1.5.3 py312h2dafd23_0
libnghttp2 1.57.0 h2d74bed_0
libsolv 0.7.24 he621ea3_0
libssh2 1.10.0 hdbd6064_2
libstdcxx-ng 11.2.0 h1234567_1
libuuid 1.41.5 h5eee18b_0
libxml2 2.10.4 hf1b16e4_1
lz4-c 1.9.4 h6a678d5_0
menuinst 2.0.2 py312h06a4308_0
ncurses 6.4 h6a678d5_0
openssl 3.0.13 h7f8727e_0
packaging 23.1 py312h06a4308_0
pcre2 10.42 hebb0a14_0
pip 23.3.1 py312h06a4308_0
platformdirs 3.10.0 py312h06a4308_0
pluggy 1.0.0 py312h06a4308_1
pybind11-abi 4 hd3eb1b0_1
pycosat 0.6.6 py312h5eee18b_0
pycparser 2.21 pyhd3eb1b0_0
pysocks 1.7.1 py312h06a4308_0
python 3.12.1 h996f2a0_0
readline 8.2 h5eee18b_0
reproc 14.2.4 h295c915_1
reproc-cpp 14.2.4 h295c915_1
requests 2.31.0 py312h06a4308_1
ruamel.yaml 0.17.21 py312h5eee18b_0
setuptools 68.2.2 py312h06a4308_0
sqlite 3.41.2 h5eee18b_0
tk 8.6.12 h1ccaba5_0
tqdm 4.65.0 py312he106c6f_0
truststore 0.8.0 py312h06a4308_0
tzdata 2023d h04d1e81_0
urllib3 2.1.0 py312h06a4308_1
wheel 0.41.2 py312h06a4308_0
xz 5.4.5 h5eee18b_0
yaml-cpp 0.8.0 h6a678d5_0
zlib 1.2.13 h5eee18b_0
zstandard 0.19.0 py312h5eee18b_0
zstd 1.5.5 hc292b87_0 5.设置镜像
(base) bio05@ecm-cefa:~$ # 使用北外的镜像
(base) bio05@ecm-cefa:~$ conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda/
(base) bio05@ecm-cefa:~$ conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/
(base) bio05@ecm-cefa:~$ conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/free/
(base) bio05@ecm-cefa:~$ conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/main/
(base) bio05@ecm-cefa:~$ conda config --set show_channel_urls yes6.安装fastqc软件
conda install fastqc -y
(base) bio05@ecm-cefa:~$ 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/bio05/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 | py312h06a4308_0 1.2 MB https://mirrors.bfsu.edu.cn/anaconda/pkgs/main
dbus-1.13.18 | hb2f20db_0 504 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
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: 371.4 MB
The following NEW packages will be INSTALLED:
dbus anaconda/pkgs/main/linux-64::dbus-1.13.18-hb2f20db_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
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-py312h06a4308~ --> anaconda/pkgs/main::conda-24.3.0-py312h06a4308_0
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done 7.查看当前conda环境
conda info -envs
(前面带*的就是当前激活的)
(base) bio05@ecm-cefa:~$ conda info --envs
# conda environments:
#
base * /home/bio05/miniconda38.创建名为rnaseq的conda环境，指定python版本是3
conda create -n rna-seq python=3 fastqc trimmomatic -y
(base) bio05@ecm-cefa:~$ conda create -n rna-seq python=3 fastqc trimmomatic -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/bio05/miniconda3/envs/rna-seq
added / updated specs:
- fastqc
- python=3
- trimmomatic(base) bio05@ecm-cefa:~$ conda info --envs
# conda environments:
#
base * /home/bio05/miniconda3
rna-seq /home/bio05/miniconda3/envs/rna-seq9.激活新的conda环境
(base) bio05@ecm-cefa:~$ conda activate rna-seq
(rna-seq) bio05@ecm-cefa:~$ fastqc
Exception in thread "main" java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
at java.desktop/java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:208)
at java.desktop/java.awt.Window.<init>(Window.java:549)
at java.desktop/java.awt.Frame.<init>(Frame.java:423)
at java.desktop/java.awt.Frame.<init>(Frame.java:388)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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