Entering edit mode
2.5 years ago
bioinformatics
▴
40
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
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.
Ok thanks, I used the following commands in the mac terminal.
conda info
(shows not installed)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.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
What you are seeing is the output of
conda info
command (posted in your original post). Soconda
is installed on your machine. That is not an error.You simply need to
activate conda
usingconda activate
command. This will activate the base environment. You will want to create/use a new environment for your RNAseq software installs.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?
conda activate
command activates thebase
environment. That is what is installed by default and will get automatically activated unless you turn it off.You should create a new envieonment when you install programs you need. for example to install
bwa
you would doOk thanks, do know what command is used to run a fastqc file e.g. SRR8668773.gkfB5so2.fastq-002.gz.part