生信星球Day3-Linux环境下的软件安装.png
linux如何安装软件？
1. 了解conda--“linux的应用商店”
1.1软件管理Miniconda
1.2conda介绍
2. 如何下载miniconda
miniconda 清华
这里犯了个错误：应该下载“Miniconda3-latest-Linux-x86_64.sh”，而不是“Miniconda3-latest-Windows-x86_64.exe”
bio04@VM-0-6-ubuntu:~/biosoft$ wget https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-latest-Linux-x86_64.sh
--2021-04-21 17:58:48-- 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-Li 100%[======================>] 89.87M 8.37MB/s in 15s
2021-04-21 17:59:04 (6.10 MB/s) - ‘Miniconda3-latest-Linux-x86_64.sh’ saved [94235922/94235922]
3. 怎么安装miniconda
bio04@VM-0-6-ubuntu:~/biosoft$ bash Miniconda3-latest-Linux-x86_64.sh
Welcome to Miniconda3 py38_4.9.2
In order to continue the installation process, please review the license
agreement.
Please, press ENTER to continue
>>>
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Last updated September 28, 2020
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':'
>>> 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 ...
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
- brotlipy==0.7.0=py38h27cfd23_1003
- ca-certificates==2020.10.14=0
- certifi==2020.6.20=pyhd3eb1b0_3
- cffi==1.14.3=py38h261ae71_2
- chardet==3.0.4=py38h06a4308_1003
- conda-package-handling==1.7.2=py38h03888b9_0
- conda==4.9.2=py38h06a4308_0
- cryptography==3.2.1=py38h3c74f83_1
- idna==2.10=py_0
- ld_impl_linux-64==2.33.1=h53a641e_7
- libedit==3.1.20191231=h14c3975_1
- libffi==3.3=he6710b0_2
- libgcc-ng==9.1.0=hdf63c60_0
- libstdcxx-ng==9.1.0=hdf63c60_0
- ncurses==6.2=he6710b0_1
- openssl==1.1.1h=h7b6447c_0
- pip==20.2.4=py38h06a4308_0
- pycosat==0.6.3=py38h7b6447c_1
- pycparser==2.20=py_2
- pyopenssl==19.1.0=pyhd3eb1b0_1
- pysocks==1.7.1=py38h06a4308_0
- python==3.8.5=h7579374_1
- readline==8.0=h7b6447c_0
- requests==2.24.0=py_0
- ruamel_yaml==0.15.87=py38h7b6447c_1
- setuptools==50.3.1=py38h06a4308_1
- six==1.15.0=py38h06a4308_0
- sqlite==3.33.0=h62c20be_0
- tk==8.6.10=hbc83047_0
- tqdm==4.51.0=pyhd3eb1b0_0
- urllib3==1.25.11=py_0
- wheel==0.35.1=pyhd3eb1b0_0
- xz==5.2.5=h7b6447c_0
- yaml==0.2.5=h7b6447c_0
- zlib==1.2.11=h7b6447c_3
The following NEW packages will be INSTALLED:
_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
brotlipy pkgs/main/linux-64::brotlipy-0.7.0-py38h27cfd23_1003
ca-certificates pkgs/main/linux-64::ca-certificates-2020.10.14-0
certifi pkgs/main/noarch::certifi-2020.6.20-pyhd3eb1b0_3
cffi pkgs/main/linux-64::cffi-1.14.3-py38h261ae71_2
chardet pkgs/main/linux-64::chardet-3.0.4-py38h06a4308_1003
conda pkgs/main/linux-64::conda-4.9.2-py38h06a4308_0
conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.7.2-py38h03888b9_0
cryptography pkgs/main/linux-64::cryptography-3.2.1-py38h3c74f83_1
idna pkgs/main/noarch::idna-2.10-py_0
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7
libedit pkgs/main/linux-64::libedit-3.1.20191231-h14c3975_1
libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2
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-6.2-he6710b0_1
openssl pkgs/main/linux-64::openssl-1.1.1h-h7b6447c_0
pip pkgs/main/linux-64::pip-20.2.4-py38h06a4308_0
pycosat pkgs/main/linux-64::pycosat-0.6.3-py38h7b6447c_1
pycparser pkgs/main/noarch::pycparser-2.20-py_2
pyopenssl pkgs/main/noarch::pyopenssl-19.1.0-pyhd3eb1b0_1
pysocks pkgs/main/linux-64::pysocks-1.7.1-py38h06a4308_0
python pkgs/main/linux-64::python-3.8.5-h7579374_1
readline pkgs/main/linux-64::readline-8.0-h7b6447c_0
requests pkgs/main/noarch::requests-2.24.0-py_0
ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.87-py38h7b6447c_1
setuptools pkgs/main/linux-64::setuptools-50.3.1-py38h06a4308_1
six pkgs/main/linux-64::six-1.15.0-py38h06a4308_0
sqlite pkgs/main/linux-64::sqlite-3.33.0-h62c20be_0
tk pkgs/main/linux-64::tk-8.6.10-hbc83047_0
tqdm pkgs/main/noarch::tqdm-4.51.0-pyhd3eb1b0_0
urllib3 pkgs/main/noarch::urllib3-1.25.11-py_0
wheel pkgs/main/noarch::wheel-0.35.1-pyhd3eb1b0_0
xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
yaml pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0
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] >>> yes
no change /home/bio04/miniconda3/condabin/conda
no change /home/bio04/miniconda3/bin/conda
no change /home/bio04/miniconda3/bin/conda-env
no change /home/bio04/miniconda3/bin/activate
no change /home/bio04/miniconda3/bin/deactivate
no change /home/bio04/miniconda3/etc/profile.d/conda.sh
no change /home/bio04/miniconda3/etc/fish/conf.d/conda.fish
no change /home/bio04/miniconda3/shell/condabin/Conda.psm1
no change /home/bio04/miniconda3/shell/condabin/conda-hook.ps1
no change /home/bio04/miniconda3/lib/python3.8/site-packages/xontrib/conda.xsh
no change /home/bio04/miniconda3/etc/profile.d/conda.csh
modified /home/bio04/.bashrc
==> For changes to take effect, close and re-open your current shell. <==
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
bio04@VM-0-6-ubuntu:~/biosoft$ source ~/.bashrc
(base) bio04@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/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
(base) bio04@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) bio04@VM-0-6-ubuntu:~/biosoft$ conda na.tsinghua.edu.cn/anaconda/cloud/conda-forge
(base) bio04@VM-0-6-ubuntu:~/biosoft$ conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
(base) bio04@VM-0-6-ubuntu:~/biosoft$ conda config --set show_channel_urls yes
4. （重点）使用miniconda
也就是查看已安装的软件、搜索、安装、卸载（生信需要的）软件，我们以fastqc为例，其实安装软件很复杂，甚至有专门的一门课来讲这个，今天这里仅是入门操作。
- 查看当前服务器上安装的所有软件列表 conda list
(base) bio04@VM-0-6-ubuntu:~/biosoft$ conda list
# packages in environment at /home/bio04/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
- 搜索conda软件 conda search xxx（软件名）
- 安装软件 conda install xxx（软件名） -y
- 不加-y版
(base) bio04@VM-0-6-ubuntu:~/biosoft$ conda install fastqc
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/bio04/miniconda3
added / updated specs:
- fastqc
The following packages will be downloaded:
package | build
---------------------------|-----------------
ca-certificates-2020.12.5 | ha878542_0 137 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
certifi-2020.12.5 | py38h578d9bd_1 143 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
conda-4.10.1 | py38h578d9bd_0 3.1 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fastqc-0.11.9 | hdfd78af_1 9.7 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
font-ttf-dejavu-sans-mono-2.37| hab24e00_0 388 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fontconfig-2.13.1 | h7e3eb15_1002 324 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
freetype-2.10.4 | h7ca028e_0 912 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
icu-67.1 | he1b5a44_0 12.9 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libiconv-1.16 | h516909a_0 1.4 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libpng-1.6.37 | h21135ba_2 306 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libuuid-2.32.1 | h14c3975_1000 26 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libxml2-2.9.10 | h68273f3_2 1.3 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
openjdk-10.0.2 | h14c3975_1015 189.2 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
openssl-1.1.1k | h27cfd23_0 2.5 MB defaults
perl-5.32.0 | h36c2ea0_0 16.8 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python_abi-3.8 | 1_cp38 4 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
------------------------------------------------------------
Total: 239.0 MB
The following NEW packages will be INSTALLED:
fastqc anaconda/cloud/bioconda/noarch::fastqc-0.11.9-hdfd78af_1
font-ttf-dejavu-s~ anaconda/cloud/conda-forge/noarch::font-ttf-dejavu-sans-mono-2.37-hab24e00_0
fontconfig anaconda/cloud/conda-forge/linux-64::fontconfig-2.13.1-h7e3eb15_1002
freetype anaconda/cloud/conda-forge/linux-64::freetype-2.10.4-h7ca028e_0
icu anaconda/cloud/conda-forge/linux-64::icu-67.1-he1b5a44_0
libiconv anaconda/cloud/conda-forge/linux-64::libiconv-1.16-h516909a_0
libpng anaconda/cloud/conda-forge/linux-64::libpng-1.6.37-h21135ba_2
libuuid anaconda/cloud/conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000
libxml2 anaconda/cloud/conda-forge/linux-64::libxml2-2.9.10-h68273f3_2
openjdk anaconda/cloud/conda-forge/linux-64::openjdk-10.0.2-h14c3975_1015
perl anaconda/cloud/conda-forge/linux-64::perl-5.32.0-h36c2ea0_0
python_abi anaconda/cloud/conda-forge/linux-64::python_abi-3.8-1_cp38
The following packages will be UPDATED:
ca-certificates pkgs/main::ca-certificates-2020.10.14~ --> anaconda/cloud/conda-forge::ca-certificates-2020.12.5-ha878542_0
certifi pkgs/main/noarch::certifi-2020.6.20-p~ --> anaconda/cloud/conda-forge/linux-64::certifi-2020.12.5-py38h578d9bd_1
conda pkgs/main::conda-4.9.2-py38h06a4308_0 --> anaconda/cloud/conda-forge::conda-4.10.1-py38h578d9bd_0
openssl 1.1.1h-h7b6447c_0 --> 1.1.1k-h27cfd23_0
Proceed ([y]/n)? y
Downloading and Extracting Packages
openjdk-10.0.2 | 189.2 MB | ######################################### | 100%
openssl-1.1.1k | 2.5 MB | ######################################### | 100%
libuuid-2.32.1 | 26 KB | ######################################### | 100%
fastqc-0.11.9 | 9.7 MB | ######################################### | 100%
ca-certificates-2020 | 137 KB | ######################################### | 100%
fontconfig-2.13.1 | 324 KB | ######################################### | 100%
perl-5.32.0 | 16.8 MB | ######################################### | 100%
freetype-2.10.4 | 912 KB | ######################################### | 100%
python_abi-3.8 | 4 KB | ######################################### | 100%
conda-4.10.1 | 3.1 MB | ######################################### | 100%
libxml2-2.9.10 | 1.3 MB | ######################################### | 100%
certifi-2020.12.5 | 143 KB | ######################################### | 100%
icu-67.1 | 12.9 MB | ######################################### | 100%
libiconv-1.16 | 1.4 MB | ######################################### | 100%
libpng-1.6.37 | 306 KB | ######################################### | 100%
font-ttf-dejavu-sans | 388 KB | ######################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
- 卸载软件 conda remove fastqc -y
5. （选修）不同的生信实战项目
需要定制conda的分身。（不理解就跳过吧）
conda 环境
- 查看当前conda有哪些环境
conda info --envs
(base) bio04@VM-0-6-ubuntu:~/biosoft$ conda info --envs
# conda environments:
#
base * /home/bio04/miniconda3
例子：处理转录组数据
- 先建立一个名叫rnaseq的conda环境；然后指定python版本是3，安装软件fastqc、trimmomatic
conda create -n rna-seq python=3 fastqc trimmomatic -y
(base) bio04@VM-0-6-ubuntu:~/biosoft$ conda create -n rna-seq python=3 fastqc trimmomatic -y
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /home/bio04/miniconda3/envs/rna-seq
added / updated specs:
- fastqc
- python=3
- trimmomatic
The following packages will be downloaded:
package | build
---------------------------|-----------------
_libgcc_mutex-0.1 | conda_forge 3 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
_openmp_mutex-4.5 | 1_gnu 22 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
certifi-2020.12.5 | py39hf3d152e_1 143 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fontconfig-2.13.1 | hba837de_1005 357 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
freetype-2.10.4 | h0708190_1 890 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
icu-68.1 | h58526e2_0 13.0 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ld_impl_linux-64-2.35.1 | hea4e1c9_2 618 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libffi-3.3 | h58526e2_2 51 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgcc-ng-9.3.0 | h2828fa1_19 7.8 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgomp-9.3.0 | h2828fa1_19 376 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libstdcxx-ng-9.3.0 | h6de172a_19 4.0 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libuuid-2.32.1 | h7f98852_1000 28 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libxml2-2.9.10 | h72842e0_4 774 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ncurses-6.2 | h58526e2_4 985 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
openssl-1.1.1k | h7f98852_0 2.1 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pip-21.0.1 | pyhd8ed1ab_0 1.1 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python-3.9.2 |hffdb5ce_0_cpython 27.3 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python_abi-3.9 | 1_cp39 4 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
readline-8.1 | h46c0cb4_0 295 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
setuptools-49.6.0 | py39hf3d152e_3 943 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
sqlite-3.35.4 | h74cdb3f_0 1.4 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tk-8.6.10 | h21135ba_1 3.2 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
trimmomatic-0.39 | hdfd78af_2 144 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
tzdata-2021a | he74cb21_0 121 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
wheel-0.36.2 | pyhd3deb0d_0 31 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xz-5.2.5 | h516909a_1 343 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
zlib-1.2.11 | h516909a_1010 106 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
------------------------------------------------------------
Total: 66.1 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex anaconda/cloud/conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex anaconda/cloud/conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
ca-certificates anaconda/cloud/conda-forge/linux-64::ca-certificates-2020.12.5-ha878542_0
certifi anaconda/cloud/conda-forge/linux-64::certifi-2020.12.5-py39hf3d152e_1
fastqc anaconda/cloud/bioconda/noarch::fastqc-0.11.9-hdfd78af_1
font-ttf-dejavu-s~ anaconda/cloud/conda-forge/noarch::font-ttf-dejavu-sans-mono-2.37-hab24e00_0
fontconfig anaconda/cloud/conda-forge/linux-64::fontconfig-2.13.1-hba837de_1005
freetype anaconda/cloud/conda-forge/linux-64::freetype-2.10.4-h0708190_1
icu anaconda/cloud/conda-forge/linux-64::icu-68.1-h58526e2_0
ld_impl_linux-64 anaconda/cloud/conda-forge/linux-64::ld_impl_linux-64-2.35.1-hea4e1c9_2
libffi anaconda/cloud/conda-forge/linux-64::libffi-3.3-h58526e2_2
libgcc-ng anaconda/cloud/conda-forge/linux-64::libgcc-ng-9.3.0-h2828fa1_19
libgomp anaconda/cloud/conda-forge/linux-64::libgomp-9.3.0-h2828fa1_19
libiconv anaconda/cloud/conda-forge/linux-64::libiconv-1.16-h516909a_0
libpng anaconda/cloud/conda-forge/linux-64::libpng-1.6.37-h21135ba_2
libstdcxx-ng anaconda/cloud/conda-forge/linux-64::libstdcxx-ng-9.3.0-h6de172a_19
libuuid anaconda/cloud/conda-forge/linux-64::libuuid-2.32.1-h7f98852_1000
libxml2 anaconda/cloud/conda-forge/linux-64::libxml2-2.9.10-h72842e0_4
ncurses anaconda/cloud/conda-forge/linux-64::ncurses-6.2-h58526e2_4
openjdk anaconda/cloud/conda-forge/linux-64::openjdk-10.0.2-h14c3975_1015
openssl anaconda/cloud/conda-forge/linux-64::openssl-1.1.1k-h7f98852_0
perl anaconda/cloud/conda-forge/linux-64::perl-5.32.0-h36c2ea0_0
pip anaconda/cloud/conda-forge/noarch::pip-21.0.1-pyhd8ed1ab_0
python anaconda/cloud/conda-forge/linux-64::python-3.9.2-hffdb5ce_0_cpython
python_abi anaconda/cloud/conda-forge/linux-64::python_abi-3.9-1_cp39
readline anaconda/cloud/conda-forge/linux-64::readline-8.1-h46c0cb4_0
setuptools anaconda/cloud/conda-forge/linux-64::setuptools-49.6.0-py39hf3d152e_3
sqlite anaconda/cloud/conda-forge/linux-64::sqlite-3.35.4-h74cdb3f_0
tk anaconda/cloud/conda-forge/linux-64::tk-8.6.10-h21135ba_1
trimmomatic anaconda/cloud/bioconda/noarch::trimmomatic-0.39-hdfd78af_2
tzdata anaconda/cloud/conda-forge/noarch::tzdata-2021a-he74cb21_0
wheel anaconda/cloud/conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
xz anaconda/cloud/conda-forge/linux-64::xz-5.2.5-h516909a_1
zlib anaconda/cloud/conda-forge/linux-64::zlib-1.2.11-h516909a_1010
Downloading and Extracting Packages
setuptools-49.6.0 | 943 KB | ######################################### | 100%
libstdcxx-ng-9.3.0 | 4.0 MB | ######################################### | 100%
readline-8.1 | 295 KB | ######################################### | 100%
libgomp-9.3.0 | 376 KB | ######################################### | 100%
xz-5.2.5 | 343 KB | ######################################### | 100%
icu-68.1 | 13.0 MB | ######################################### | 100%
openssl-1.1.1k | 2.1 MB | ######################################### | 100%
python-3.9.2 | 27.3 MB | ######################################### | 100%
wheel-0.36.2 | 31 KB | ######################################### | 100%
fontconfig-2.13.1 | 357 KB | ######################################### | 100%
_openmp_mutex-4.5 | 22 KB | ######################################### | 100%
ncurses-6.2 | 985 KB | ######################################### | 100%
libuuid-2.32.1 | 28 KB | ######################################### | 100%
ld_impl_linux-64-2.3 | 618 KB | ######################################### | 100%
freetype-2.10.4 | 890 KB | ######################################### | 100%
python_abi-3.9 | 4 KB | ######################################### | 100%
certifi-2020.12.5 | 143 KB | ######################################### | 100%
tk-8.6.10 | 3.2 MB | ######################################### | 100%
sqlite-3.35.4 | 1.4 MB | ######################################### | 100%
libffi-3.3 | 51 KB | ######################################### | 100%
zlib-1.2.11 | 106 KB | ######################################### | 100%
trimmomatic-0.39 | 144 KB | ######################################### | 100%
_libgcc_mutex-0.1 | 3 KB | ######################################### | 100%
libxml2-2.9.10 | 774 KB | ######################################### | 100%
tzdata-2021a | 121 KB | ######################################### | 100%
pip-21.0.1 | 1.1 MB | ######################################### | 100%
libgcc-ng-9.3.0 | 7.8 MB | ######################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate rna-seq
#
# To deactivate an active environment, use
#
# $ conda deactivate
-再次查看一下我们的conda环境，conda info --envs ，看是不是多了一个rna-seq。但是发现，默认还是base
(base) bio04@VM-0-6-ubuntu:~/biosoft$ conda info --envs
# conda environments:
#
base * /home/bio04/miniconda3
rna-seq /home/bio04/miniconda3/envs/rna-seq
-激活新的conda环境 conda activate rna-seq
(base) bio04@VM-0-6-ubuntu:~/biosoft$ conda activate rna-seq
(rna-seq) bio04@VM-0-6-ubuntu:~/biosoft$
- 显示帮助文档
随便输入一个软件名称
(rna-seq) bio04@VM-0-6-ubuntu:~/biosoft$ fastqc
Exception in thread "main" java.lang.UnsatisfiedLinkError: /home/bio04/miniconda3/envs/rna-seq/lib/libawt_xawt.so: libXrender.so.1: cannot open shared object file: No such file or directory
at java.base/java.lang.ClassLoader$NativeLibrary.load0(Native Method)
at java.base/java.lang.ClassLoader$NativeLibrary.load(ClassLoader.java:2424)
at java.base/java.lang.ClassLoader$NativeLibrary.loadLibrary(ClassLoader.java:2481)
at java.base/java.lang.ClassLoader.loadLibrary0(ClassLoader.java:2678)
at java.base/java.lang.ClassLoader.loadLibrary(ClassLoader.java:2611)
at java.base/java.lang.Runtime.load0(Runtime.java:814)
at java.base/java.lang.System.load(System.java:1838)
at java.base/java.lang.ClassLoader$NativeLibrary.load0(Native Method)
at java.base/java.lang.ClassLoader$NativeLibrary.load(ClassLoader.java:2424)
at java.base/java.lang.ClassLoader$NativeLibrary.loadLibrary(ClassLoader.java:2481)
at java.base/java.lang.ClassLoader.loadLibrary0(ClassLoader.java:2678)
at java.base/java.lang.ClassLoader.loadLibrary(ClassLoader.java:2632)
at java.base/java.lang.Runtime.loadLibrary0(Runtime.java:876)
at java.base/java.lang.System.loadLibrary(System.java:1875)
at java.desktop/java.awt.Toolkit$3.run(Toolkit.java:1395)
at java.desktop/java.awt.Toolkit$3.run(Toolkit.java:1393)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.desktop/java.awt.Toolkit.loadLibraries(Toolkit.java:1392)
at java.desktop/java.awt.Toolkit.<clinit>(Toolkit.java:1425)
at java.desktop/java.awt.Component.<clinit>(Component.java:590)
-退出当前环境 conda deactivate
