Set up conda rna seq analysis

Question

[bioinformatics]

Hi,

I'm trying to set up miniconda on a mac for rna seq analysis. However I keep getting the error message (conda not installed):

   active environment : base
    active env location : /Users/mesalie/miniconda
            shell level : 1
       user config file : /Users/mesalie/.condarc
 populated config files : /Users/mesalie/.condarc
          conda version : 4.12.0
    conda-build version : not installed
         python version : 3.9.12.final.0
       virtual packages : __osx=10.13.6=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /Users/mesalie/miniconda  (writable)
      conda av data dir : /Users/mesalie/miniconda/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/osx-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/mesalie/miniconda/pkgs
                          /Users/mesalie/.conda/pkgs
       envs directories : /Users/mesalie/miniconda/envs
                          /Users/mesalie/.conda/envs
               platform : osx-64

Could someone please advise me on how to correct this error message.

Thanks

[MatthewP]

Hi, we can't give any advice without knowing what you tried (your commands/codes), and you need to format your error messages in a code block.
Press "Code Sample" above to insert error messages.

[bioinformatics]

Ok thanks, I used the following commands in the mac terminal.

bash ~/Miniconda3-latest-MacOSX-x86_64.sh -b -p $HOME/miniconda 
source $HOME/miniconda/bin/activate 

conda init zsh

conda info (shows not installed)

[MatthewP]

I don't know mac. Did you confirm your miniconda installation has no error? Maybe You need to reopen your terminal after conda init zsh, this is required in linux.

[bioinformatics]

I tried to reopen the terminal and it didn't reopen. I’m trying to install Miniconda and received an error message. I’m following the protocol on protocols.hostmicrobe.org/conda

[GenoMax]

What you are seeing is the output of conda info command (posted in your original post). So conda is installed on your machine. That is not an error.

You simply need to activate conda using conda activatecommand. This will activate the base environment. You will want to create/use a new environment for your RNAseq software installs.

[bioinformatics]

Ok thanks I think it says Conda build version is not installed. Hopefully that does not affect the analysis. Did you know what the command is for Conda activate?

[GenoMax]

conda activate command activates the base environment. That is what is installed by default and will get automatically activated unless you turn it off.

conda config --set auto_activate_base false

You should create a new envieonment when you install programs you need. for example to install bwa you would do

conda create -n rnaseq bwa samtools
conda activate rnaseq # to use the programs

[bioinformatics]

Ok thanks, do know what command is used to run a fastqc file e.g. SRR8668773.gkfB5so2.fastq-002.gz.part