bash: conda: command not found | for SimLord [CLOSED]

Question

[Anonymous]

I am now using an alternative called FASTQC.

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I've successfully installed MiniConda and ran its .exe. It established C:/Users/User/miniconda3.

I'm following along with SimLord tutorial, that requires MiniConda.

cding to C:/Users/User/miniconda3 - I run the first command in Bash:

>>>conda create -n simlord python=3 pip numpy scipy cython
bash: conda: command not found

How can I rectify this? Sorry if it's something obvious.

Answer 1

[GenoMax]

>>> in your conda line seems to indicate that you have logged into python interpreter. Exit back out to the shell prompt using quit().

I believe that conda offers to modify your $PATH at the end of the installation so the executable is available. Otherwise find where it is located and add that directory to your $PATH.

It appears that you are doing this on Windows due to the C:/ path specification. Certain programs may not be supported on windows though simlord seems to indicate that it may work as long as python3 and other dependencies are available.

[Anonymous]

$ quit()
> conda create -n simlord python=3 pip numpy scipy cython

bash: syntax error near unexpected token `conda'

[GenoMax]

Unclear what you are showing us here. I assume with quit() you are back on the command prompt. Which command prompt is that? Is that from windows or from Windows subsystem for Linux (WSL).

[Anonymous]

Hi, I am new and unsure of any of this. I have however been successful at installing an alternative called FASTQC, and can open my .fastq file here. Thank you for your responses.