Conda in offline envs - core-unit-bioinformatics/knowledge-base GitHub Wiki
- You want to create a conda environment on a compute infrastructure without internet access
- typical scenario: HPCs / compute clusters
- Create the Conda environment on a different system (e.g., your laptop), pack it, transfer it to the offline system and unpack it.
- If the offline infrastructure offers local mirrors to popular Conda channels such as
conda-forgeorbioconda, making use of those channel mirrors typically requires configuring your.condarcfile in a specific way.
More info in the official docs: docs.conda.io
Important Several .condarc files may exist in your environment. Locate all active ones as follows:
$ conda config --show-sources
# prints something like the following on your screen
==> /home/YOURUSER/.condarc <== # standard .condarc location in $HOME
add_pip_as_python_dependency: True
allow_softlinks: False
auto_update_conda: False
env_prompt: ({name})
default_threads: 2
envs_dirs:
- /your/system/path/to/conda/installation/envs # default location for conda envs
pkgs_dirs:
- /your/system/path/to/conda/installation/pkgs # default location to store downloaded package data
channel_priority: strict
channels:
- https://conda.anaconda.org/conda-forge # example: default channel URL that requires internet access
- https://conda.anaconda.org/bioconda
- nodefaults
allowlist_channels:
- https://conda.anaconda.org/conda-forge
- https://conda.anaconda.org/bioconda
- nodefaults
denylist_channels:
- defaults
always_yes: FalseIf several .condarc files are found, delete or rename all but one (preferably, the one in your $HOME)
to avoid configuration conflicts because all .condarc files will be parsed and evaluated
(precedence depends on parsing order).
Note that the infrastructure admins may set a system-wide .condarc file, which would normally be protected
from any changes by unprivileged users.
Only for HHU members
- HILBERT offers Conda channel mirrors; please find the official documentation in the HHU Wiki.
On HILBERT, a valid .condarc file may look like this:
HILBERT $ conda config --show-sources
==> /home/YOURUSER/.condarc <==
allow_softlinks: False
auto_update_conda: False
auto_activate_base: False
env_prompt: ({name})
envs_dirs:
- /your/system/path/to/conda/installation/envs
pkgs_dirs:
- /your/system/path/to/conda/installation/pkgs
channel_priority: strict
channels:
- http://conda.repo.test.hhu.de/conda-forge # example: URL of channel mirror that is reachable from HILBERT
- http://conda.repo.test.hhu.de/bioconda
- http://conda.repo.test.hhu.de/main
show_channel_urls: True