Issues Setting Up

[Cmbarrows]

Hello,

I hope this is okay but I wanted to provide some feedback in setting up the computer. I am a novice and really struggled despite following the directions. I am using a windows computer (windows 10 - education) with the Ubuntu installation through the microsoft store.

The first issue I had was a the http error many other users seem to be getting with the SSL issues. Specifically the "HTTP 000 CONNECTION FAILED for url".

What I tried: all of the resolutions including setting the ssl_verify to "false" and "no" with no success. Turning off my firewall. Uninstalling and reinstalling. What worked: Installing the program by Shining Light Productions "Win64 OpenSSL v3.0.0 Light".

The second issue I had was installing all the tools. Specifically the error messages "Encountered problems while solving: -nothing provides requested seqkit -nothing provides requested ..." - I wont list them all.

What I tried: the resolutions suggested that the install went into the base configuration and not the bioinfo one, which wasn't the case because I ran the script "conda activate bioinfo" before trying to install. Other solutions suggested instructions for setting up the bash initialization scripts weren't followed as detailed in the second part of the Installation chapter, but again I did all those steps. What worked: running the following two scripts. conda config --add channels bioconda conda config --add channels conda-forge

Anyway, these solutions were not easy to find (but super easy to apply). I'm not sure why I had so many issues. Hoping this is either useful to someone or makes its way into the book for those of us who could not get the install working. Adding these to the "how to fix problems" chapter and the solutions that work would be super helpful. Digging through closed issues was challenging because many solutions were not written for a new user like deleting specific files or changing path names.

[ialbert]

Thanks for the note,

First I am happy to see that you worked out the problems. That is commendable.

But I want to make a correction. The installation instructions in the book do contain the section on adding bioconda channels. In the chapter titled "How to install conda and mamba" there is a subsection titled "What is bioconda?" that states:

Bioconda is a channel for distributing bioinformatics software that can be enabled in the Conda package manager. Run the following in your terminal:

conda config --add channels bioconda
conda config --add channels conda-forge

The bioconda channel is now active within the conda package manager.

Perhaps I should make that section a bit more prominent as it can be missed.

Now when it comes to the HTTP errors, unfortunately it is not really clear what causes that error, I am glad you figured out a solution. But is a quite uncommon situation. In my last cohort of 40 students that have recently all gone through the installation, no one ran into that problem. It seems it may happen for various reasons as demonstrated in the question:

https://stackoverflow.com/questions/42563757/conda-update-condahttperror-http-none

I suspect that you may have multiple versions of conda running, perhaps a windows version and a UNIX version or something similar and those interact in some manner. The fact that you had to install a windows tool when working via UNIX is a bit odd, to be honest, it makes no sense, since your Unix environment ought to be separate from the Windows one. Hence I suspect you may be running the windows version of conda.

But I am happy that you all worked it out, and we'll keep this issue here for future reference.

[Cmbarrows]

My apologies! I did the conda config the first time but not after the reinstall. I jumped right back to installing Mamba after installing conda which is where I ran into the first http error.

I am so sorry.

I am nervous about potentially running a windows version of conda and not the Unix version. I suspect that will create issues later down the line. Is there a way to check and/or fix it?

[ialbert]

you can check with the command:

which conda

[troysgit]

Had the same issues as OP and appreciate the solutions with the two conda config --add channels.

[ialbert]

There is now a new page with step-by-step installation instructions for troubleshooting the quick setup

https://www.biostarhandbook.com/step-by-step.html

[originade]

I had this error today. I narrowed it down to step #6 "Update conda" as well as skipping to step #7 "Install mamba" (for troubleshooting purposes). I followed all steps in order and the suggestions in this thread and other posts.

I resolved the issue from this comment by touching the files: https://github.com/conda/conda/issues/9948#issuecomment-909989810 I had to do it twice, one to update conda and the second time to install mamba. After that the rest of the manual step by step installation worked.

[ialbert]

thanks for following this up with a detailed explanation,

the problem looks to be more complex, I will add link to you troubleshooting solution to the book. A small but consistent percent of people do report the mysterious

HTTP 000 CONNECTION FAILED for URL

error that so far I never understood the reasons for,

the issue you found shows a more complicated cause

[originade]

There are many potential solutions in the thread I linked previously from downgrading anaconda versions (not ideal) or installing a previous version then updating, chmod 777 the anaconda directory, completely restarting the WSL, or touching the files as I did (probably the easiest solution). People seem to think it's a WSL issue with conda.

If anyone is having this HTTP 000 error, I would check out that thread for potential solutions: https://github.com/conda/conda/issues/9948#issuecomment-909989810

I'm glad you've linked it in the book. Thanks!