fastq-dump (or any command line tool) not found

Question

[Jeffrey]

Please help. I am trying to get started in bioinformatics and having trouble getting an environment set up. I am using Ubuntu. I installed anaconda and created a new environment. I added sra toolkit to the environment. I opened a jupyter notebook in that environment and tried to use sra-toolkit commands such as fastq-dump, but I get "command not found". What do I have to do to make packages I installed to my environment visible in jupyter notebook?

[Giulia.cosenza]

Why do you have to use it on Jupyter-notebook? You can use sratoolkit from terminal.

I imagine you need the command to download fastq files starting from a file.sra, and you what to use the downloaded file on Jupyter notebook.

You simply have to follow the following command on terminal:

cd $path_to_the_folder_where_you_whant_your_downloads_to_be_set

conda activate $conda_environment_with_sratoolkit_installed

fastq-dump --split-files file.sra

conda activate $conda_environment_with_jupyter_installed

jupyter notebook

Once on your notebook you can upload the fastq like this

file= glob.glob("*.fastq")

[Jeffrey]

First, thank you for the response. Well, I'd like to use jupyter notebook as I learn bioinformatics so that I have a record of everything I've done. It was my understanding that I could run command line tools from within a jupyter notebook. I thought that I could click the "white triangle in a green circle" next to my environment in anaconda navigator and start a jupyter notebook in that environment. Maybe my problem is that I'm not really in that environment and that is why the commands are not found?

Here is exactly what I am trying to do. I am trying to learn chip-seq data analysis by following the steps in the book, "Practical Guide to Chip-seq Analysis". On page 15 it tells me to enter this command: fastq-dump --origfmt --outdir data --gzip -A SRR250083

So, using anaconda navigator, I created an environment and installed SRA toolkit. I thought I would then be able to launch jupyter notebook in that environment and run the command like this:

!fastq-dump --origfmt --outdir data --gzip -A SRR250O83

It tells me fastq-dump not found. If I enter !fastq-dump -h it tells me fastq-dump not found. I guess the particular command isn't important. The problem is that it can't find the sra-toolkit tools I installed in my environment, and I don't know why.

Answer 1

[Jeffrey]

I think I found a solution. Even though I chose to launch jupyter notebook from the environment where I installed the sra toolkit, it seems that anaconda navigator launched jupyter notebook in my base environment which didn't have sra toolkit installed. So, what I had to do was activate the correct conda environment from within the jupyter notebook. Then, the tools I installed were found.