anaconda base环境_我的服务器conda环境配置方法

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

chmod +x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh

# 设置
Do you accept the license terms? [yes|no]
[no] >>> yes

Miniconda3 will now be installed into this location:
/home/zhaohuanan/miniconda3

  - Press ENTER to confirm the location
  - Press CTRL-C to abort the installation
  - Or specify a different location below

[/home/zhaohuanan/miniconda3] >>> /home/zhaohuanan/zhaohn_HD/miniconda3



Preparing transaction: done
Executing transaction: done
installation finished.
WARNING:
    You currently have a PYTHONPATH environment variable set. This may cause
    unexpected behavior when running the Python interpreter in Miniconda3.
    For best results, please verify that your PYTHONPATH only points to
    directories of packages that are compatible with the Python interpreter
    in Miniconda3: /home/zhaohuanan/zhaohn_HD/miniconda3
Do you wish the installer to initialize Miniconda3
by running conda init? [yes|no]
[no] >>> yes

# 首先将bashrc或者zshrc中 conda init的部分全部删掉！
# 然后

# if you use BASH: your_anaconda_path/bin/conda init bash
/home/zhaohuanan/zhaohn_HD/miniconda3/bin/conda init bash

# if you use zsh: your_anaconda_path/bin/conda init zsh
# 我喜欢用zsh所以会用下面的
/home/zhaohuanan/zhaohn_HD/miniconda3/bin/conda init zsh



# 如果遇到conda没有权限的问题
# zsh: permission denied: /home/zhaohuanan/zhaohn_HD/miniconda3/bin/conda
# 先执行
chmod -R +x /home/zhaohuanan/zhaohn_HD/miniconda3/bin
# 再执行
/home/zhaohuanan/zhaohn_HD/miniconda3/bin/conda init zsh




# state:

no change     /home/zhaohuanan/zhaohn_HD/miniconda3/condabin/conda
no change     /home/zhaohuanan/zhaohn_HD/miniconda3/bin/conda
no change     /home/zhaohuanan/zhaohn_HD/miniconda3/bin/conda-env
no change     /home/zhaohuanan/zhaohn_HD/miniconda3/bin/activate
no change     /home/zhaohuanan/zhaohn_HD/miniconda3/bin/deactivate
no change     /home/zhaohuanan/zhaohn_HD/miniconda3/etc/profile.d/conda.sh
no change     /home/zhaohuanan/zhaohn_HD/miniconda3/etc/fish/conf.d/conda.fish
no change     /home/zhaohuanan/zhaohn_HD/miniconda3/shell/condabin/Conda.psm1
no change     /home/zhaohuanan/zhaohn_HD/miniconda3/shell/condabin/conda-hook.ps1
no change     /home/zhaohuanan/zhaohn_HD/miniconda3/lib/python3.8/site-packages/xontrib/conda.xsh
no change     /home/zhaohuanan/zhaohn_HD/miniconda3/etc/profile.d/conda.csh
modified      /home/zhaohuanan/.zshrc

==> For changes to take effect, close and re-open your current shell. <==

# 清除之前残留的conda channels
rm -rf ~/.condarc

# 按顺序依次添加channel
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda config --add channels r
# 不喜欢清华源，常常挂掉；
# 使用mamba的话即使用官方源，速度也是ok的，省去了很多麻烦；

# 接下来查看自己已添加的源
conda config --get channels
# return
--add channels 'defaults'   # lowest priority
--add channels 'conda-forge'
--add channels 'bioconda'
--add channels 'r'   # highest priority


cat ~/.condarc
# return
channels:
  - r
  - bioconda
  - conda-forge
  - defaults
# 也就是说最后添加的channel会拥有最高优先级，在condarc中越靠前的channel优先级也就越高

# (base)
conda install -c conda-forge mamba

mamba update -n base -c defaults conda

# 执行
chown -R your_user_name your_anaconda_path
chmod -R +rX your_anaconda_path
# 如
chown -R zhaohuanan /home/zhaohuanan/zhaohn_HD/miniconda3
chmod -R +rxX /home/zhaohuanan/zhaohn_HD/miniconda3

# (base)
mamba install screen ncdu htop jupyterlab r=4.0 
fastqc multiqc cutadapt 
bwa bowtie bowtie2 hisat2 
samtools sambamba bedtools vcftools bcftools deeptools subread 
samclip parallel-fastq-dump 
pandas numpy scipy biopython pysam matplotlib 
snakemake