Today we continued to learn about how to use Linux in an online server.

Day 3

First step: install bzip2

Try to enter bzip2 within Linux environment, and see the response.
If bzip2 hasn't been installed, then install it using the following commend:

yum install -y bzip2

Second step: access Miniconda

Access the online server and go to the file "biosoft" as created yesterday by the commend below:

cd biosoft

Go to Miniconda download website via Google, and find the the downloadable version which fits your Linux version. Then click "copy the download link". Using the commend below within Linux environment to download Miniconda (given the link is https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh):

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

Then use the following commend to install it:

bash Miniconda3-latest-Linux-x86_64.sh

Then activate Miniconda by the following commend:

source ~/.bashrc

Use the following commends if you are in China:

conda config --add channels https://mirrors.ustc.edu.cn/anaconda/pkgs/free
conda config --add channels https://mirrors.ustc.edu.cn/anaconda/pkgs/main/
conda config --add channels https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/
conda config --add channels https://mirrors.ustc.edu.cn/anaconda/cloud/bioconda/
conda config --set show_channel_urls yes

Third step: use Miniconda

To see you what contents are in your conda list:

conda list

To search a software (ie fastqc):

conda search fastqc

To install a software (ie fastqc):

conda install fastqc -y

To uninstall a software (ie fastqc):

conda remove fastqc -y

Fourth step: conda environment

To see what conda environments do you currently have:

conda info --envs

To create an environment named "rna-seq" and install two softwares "fastqc" and "trimmomatic" given the version of python is 3:

conda create -n rna-seq python=3 fastqc trimmomatic -y

To activate the new environment "rna-seq":

source activate rna-seq

To uninstall a software:

conda remove -n rna-seq fastqc -y

To uninstall all softwares in a given environment:

conda remove -n rna-seq --all