micromamba activate code

[crabeyko-afk]

$ curl http://data.biostarhandbook.com/install.sh | bash
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  4503  100  4503    0     0  37814      0 --:--:-- --:--:-- --:--:-- 37840
#
# Welcome to the Biostar Handbook!
#
# Web: https://www.biostarhandbook.com/
#
# Setting up bioinformatics tools.
#
# 1. Installing micromamba
#
# 2. Configuring micromamba channels
#
# 3. Configuring the shell
#
Running `shell init`, which:
# 5. Installing tools into bioinfo
#
warning  libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.
    
warning  libmamba Please make sure you understand Anaconda Terms of Services.
    
warning  libmamba See: https://legal.anaconda.com/policies/en/
# 6. Installing doctor.py
#
# 7. Installing the bio package
#
# 8. Installing Entrez Direct
#
# 9. Installing the SRA toolkit
#
# The Biostar Handbook software installation has completed!
#
# Restart the terminal or type: source ~/.bash_profile
#
(base) 
heshansandeepa@Heshans-MacBook-Air-2 ~
$ doctor.py
# Doctor! Doctor! Give me the news.
# Checking symptoms ...
# bwa           --> ERROR
# datamash      --> ERROR
# fastqc -h     --> ERROR
# hisat2        --> ERROR
# featureCounts --> ERROR
# efetch        ... OK
# esearch       ... OK
# samtools      --> ERROR
# fastq-dump    ... OK
# bowtie2       --> ERROR
# bcftools      --> ERROR
# seqtk         --> ERROR
# seqkit        --> ERROR
# bio           ... OK
# fastq-dump -X 1 -Z SRR1553591 ... OK
#
# Found some problems
#
# Unable to run: bwa, datamash, fastqc -h, hisat2, featureCounts, samtools, bowtie2, bcftools, seqtk, seqkit
#
# Check the Biostar Handbook for installation help.
#
(base) 
heshansandeepa@Heshans-MacBook-Air-2 ~
$ micromamba activate bioinfo

EnvironmentNameNotFound: Could not find conda environment: bioinfo
You can list all discoverable environments with `conda info --envs`.


(base) 
heshansandeepa@Heshans-MacBook-Air-2 ~
$ 
(base) 
heshansandeepa@Heshans-MacBook-Air-2 ~
$ micromamba --version
conda 25.7.0
(base) 
heshansandeepa@Heshans-MacBook-Air-2 ~.                                                                                  

i was able to install the biostarhand book successfully. but when i try to run the "$ micromamba activate bioinfo" , i received "EnvironmentNameNotFound" output. but in my MacOS has already installed micromamba. (i have pasted the code and result i got in this text box.)
could you please anyone help me to figure out this?
(I am at very begginer level of this coding thing )

[ialbert]

Here it seems you already had conda installed so it seems there is a conflict between conda and micromamba.

Both conda and micromamba are the same tool basically, just different versions of it.

Note that when you ask for

micromamba --version

the answer is conda

conda 25.7.0

There is no easy solution here, it is all about local configuration and the two installers stepping on each other.

I will modify the installer to refuse to run if a user already has conda installed.

[ialbert]

What I would do is edit the .bashrc or .bash_profile that has the conda initialization to disable conda and keep only micromamba.