Bioconda

Bioconda

1. Install

Location: link for Miniconda

# this script might not work now
curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh

For Zsh environment

Conda would add code for initiate it at the end of the .bashrc. You may need to copy them in to the ~/.zshrc if you are using zsh.

An example of codes after you run cat ~/.bashrc

And then, you can start the conda by `source ~/.zshrc` or open a new terminal.

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

2. Setup Channels

You may need to add the bin file in your environment

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Virtual Environment

## Create an environment
conda create -n Biostation python=3.7

## Check the env list
conda env list

## 激活工作环境，需要几十秒
source activate Biostation
##or
conda activate Biostation

## 关闭工作环境：不用时关闭，不然你其它程序可能会出错
source deactivate
## Or
conda deactivate

Install into Non-default Location

Reference: saturncloud

# you can use --prefix or -p to replace the -n/--name
conda create --prefix /path/to/directory python=3.8 numpy

# this is how you can activate this environment
conda activate /path/to/directory

Delete you Environment

conda remove --name snpeff --all

Common Software for Bioinformatics

conda install fastqc
conda install fastp
conda install trimmomatic
conda install bowtie
conda install bowtie2
conda install samtools

Error

UnavailableInvalidChannel: The channel is not accessible or is invalid.
  channel name: miniconda/cloud/bioconda
  channel url: https://mirrors.bfsu.edu.cn/miniconda/cloud/bioconda
  error code: 404

You will need to adjust your conda configuration to proceed.
Use `conda config --show channels` to view your configuration's current state,
and use `conda config --show-sources` to view config file locations

Solving his by run:
conda config --remove-key channels

GLIBC_2.17

ImportError: /lib64/libc.so.6: version 'GLIBC_2.14' not found
ImportError: /lib64/libc.so.6: version 'GLIBC_2.15' not found
ImportError: /lib64/libc.so.6: version 'GLIBC_2.17' not found

This error is very wired. When you have sudo right, you can solve it easily. But when you don’t have sudo right, I believe that the quickest way to “solve”, bypass actually, this problem is down-grade your libraries. Most of time, the conflict comes from zlib and Xz. This is not the only way to solve it in CentOS 6.

conda install Xz==5.2.3 zlib==1.2.8 #numpy==1.9.3