conda测试2019镜像问题

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最近很多人反映conda镜像挂掉的问题，所以我有必要给粉丝测试一下：

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

代码正常安装即可！

万一你没有把conda添加到环境变量，也可以重新安装，或者修改bashrc咯，我这里测试的用户就是 Ubuntu用户。

no change /home/ubuntu/miniconda3/condabin/conda
no change /home/ubuntu/miniconda3/bin/conda
no change /home/ubuntu/miniconda3/bin/conda-env
no change /home/ubuntu/miniconda3/bin/activate
no change /home/ubuntu/miniconda3/bin/deactivate
no change /home/ubuntu/miniconda3/etc/profile.d/conda.sh
no change /home/ubuntu/miniconda3/etc/fish/conf.d/conda.fish
no change /home/ubuntu/miniconda3/shell/condabin/Conda.psm1
no change /home/ubuntu/miniconda3/shell/condabin/conda-hook.ps1
no change /home/ubuntu/miniconda3/lib/python3.7/site-packages/xonsh/conda.xsh
no change /home/ubuntu/miniconda3/etc/profile.d/conda.csh
modified /home/ubuntu/.bashrc

这个文件被修改的很复杂，一般人可能是看不懂的，当然，也不需要懂。

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/ubuntu/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
 eval "$__conda_setup"
else
 if [ -f "/home/ubuntu/miniconda3/etc/profile.d/conda.sh" ]; then
 . "/home/ubuntu/miniconda3/etc/profile.d/conda.sh"
 else
 export PATH="/home/ubuntu/miniconda3/bin:$PATH"
 fi
fi
unset __conda_setup

默认的镜像可以查看： conda config --show channels

conda的base环境可以被抑制

这样就不用担心conda污染我们的系统了

source /home/ubuntu/.bashrc
conda config --set auto_activate_base false

尝试下载安装

首先测试 conda install numpy 发现速度非常棒！

 blas pkgs/main/linux-64::blas-1.0-mkl
 intel-openmp pkgs/main/linux-64::intel-openmp-2019.3-199
 libgfortran-ng pkgs/main/linux-64::libgfortran-ng-7.3.0-hdf63c60_0
 mkl pkgs/main/linux-64::mkl-2019.3-199
 mkl_fft pkgs/main/linux-64::mkl_fft-1.0.12-py37ha843d7b_0
 mkl_random pkgs/main/linux-64::mkl_random-1.0.2-py37hd81dba3_0
 numpy pkgs/main/linux-64::numpy-1.16.3-py37h7e9f1db_0
 numpy-base pkgs/main/linux-64::numpy-base-1.16.3-py37hde5b4d6_0

这个 mkl-2019.3 | 203.3 MB 都是几秒钟就下载OK了。

再尝试fastqc等生物信息学软件。

conda deactivate
conda create -n qc
conda activate qc
conda info
conda install fastqc -c bioconda

速度也飞快，这个时候我的镜像是：

custom_channels:
 pkgs/main: https://repo.anaconda.com
 pkgs/free: https://repo.anaconda.com
 pkgs/r: https://repo.anaconda.com
 pkgs/pro: https://repo.anaconda.com
custom_multichannels:
 defaults:
 - https://repo.anaconda.com/pkgs/main
 - https://repo.anaconda.com/pkgs/free
 - https://repo.anaconda.com/pkgs/r
 local:
debug: False
default_channels:
 - https://repo.anaconda.com/pkgs/main
 - https://repo.anaconda.com/pkgs/free
 - https://repo.anaconda.com/pkgs/r
default_python: 3.7

尝试修改镜像

首先看看清华镜像

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 config --show channels
conda deactivate
conda create -n qinghua
conda activate qinghua
conda install fastqc -c bioconda

虽然慢了一点，但实际上还是可以使用的！

值得一提的是这个时候安装的是 openjdk-11.0.1 ， 而 默认镜像安装的是：openjdk-8.0.152

再 看看腾讯的镜像：

conda config --add channels https://mirrors.cloud.tencent.com/anaconda/pkgs/free/
conda config --add channels https://mirrors.cloud.tencent.com/anaconda/cloud/bioconda/
conda config --add channels https://mirrors.cloud.tencent.com/anaconda/cloud/msys2/
conda config --add channels https://mirrors.cloud.tencent.com/anaconda/cloud/menpo/
conda config --add channels https://mirrors.cloud.tencent.com/anaconda/cloud/peterjc123/
conda config --add channels https://mirrors.cloud.tencent.com/anaconda/pkgs/main/
conda config --add channels https://mirrors.cloud.tencent.com/anaconda/cloud/conda-forge/
conda config --add channels https://mirrors.cloud.tencent.com/anaconda/cloud/pytorch/
conda config --set show_channel_urls yes
conda config --show channels
conda deactivate
conda create -n tercent -y 
conda activate tercent 
conda install fastqc -c bioconda

是不可访问的！！

删除已经添加的镜像

既然腾讯镜像错误，那么就需要删除，其实就是编辑 文件 ~/.condarc 即可

conda config --show channels
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