[bioconda] The channel is not accessible or is invalid.

Question

[kenichi.miyata]

Hey everyone!

I cannot install bioinformatics software (samtools and so on...) through BIOCONDA. I'm in trouble!

To use bioconda (to install bioinformatics software), I installed the latest Miniconda3 according to the official homepage (https://bioconda.github.io/user/install.html).

Although I could install Miniconda3, I cannot install bioinformatics packages through bioconda. I can install packages other than bioinformatical packages through Miniconda3.

For example,

$ conda install -c bioconda samtools

Collecting package metadata (current_repodata.json): failed

UnavailableInvalidChannel: The channel is not accessible or is invalid.
  channel name: bioconda
  channel url: https://conda.anaconda.org/bioconda
  error code: 404
You will need to adjust your conda configuration to proceed.
Use `conda config --show channels` to view your configuration's current state,
and use `conda config --show-sources` to view config file locations.

$ conda config --show channels

channels:
  - bioconda
  - r
  - defaults
  - conda-forge

$ conda config --show-sources

==> /Users/miyatakenichi/.condarc <==
channels:
  - bioconda
  - r
  - defaults
  - conda-forge

Using machine is MacBook Pro (macOS BigSur v11.2.3)

[hugo.avila]

Hi ! You also could try to use mamba a reimplementation of conda in C++. Just install it in your conda base env and then replace conda by mamba like this:

# first install (at your base env):
conda install mamba

# use it:
mamba create -n my_env
mamba activate my_env
mamba install samtools

# or
mamba create -n my_env samtools -y

Mamba is a parallelized faster conda. It facilitates alot the build of new envs in personal computers and servers. A lot a times (not like this one that the serves were down) problems can be solved by just using mamba.

[kenichi.miyata]

Thank you very much for your valuable information!

Answer 1

[Kevin Blighe]

FYI, you will currently be unable to install any Bioconda packages. There's something wrong with the index on Anaconda's servers. They're aware of the issue and are working on it.

— Devon Ryan (@dpryan79) November 9, 2021

[kenichi.miyata]

That's surprising! Thank you very much for your valuable information, Kevin!