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Re: Refs to Conda - gone through the med/bio task list

On 18/10/2019 13:06, Steffen Möller wrote:
In summary, I think the effort should be continued. I feel personally somewhat responsible for the packages in our bio-* task lists. Beyond that, we either convince our community that the effort is worth it - or likely it is not worth it. Without examples how this all can be brought to some good use, we should possibly invest our energy elsewhere.

Hi, Steffen.

I install a shared copy of "bioconda" in /opt and use a wrapper to avoid conflicts between OS versions of the Python scripts and libraries and any versions that are dependencies of particular "conda" environments:

#@(#)bioconda3.sh  2019-02-23  A.J.Travis

# Wrapper for Bioconda Python environment

exec /bin/bash --rcfile /usr/local/bin/bioconda3.rc

#@(#)bioconda3.rc  2019-10-09  A.J.Travis

# Wrapper for Bioconda Python environment

eval "$(/opt/bioconda3/bin/conda shell.bash hook)"

[And a similar wrapper for "bioconda2"]

One reason for using "bioconda" is that it makes it practical to have multiple versions of applications installed, which is often important (e.g. to complete a project using the same version of an application, while upgrading the system to use the latest version for new projects.

However, it's a recipe for disaster to follow the default "miniconda" bootstrap instructions that modify ".bashrc" (or the profile of the shell you are using) and duplicate the entire "bioconda" installation for each user in their own login directory.

Using a shared installation is better, but needs to be done using a wrapper to avoid breaking the OS environment for "root" and similarly the 'normal' login environment for other users, who can still add their own environments without needlessly duplicating the core applications.

I also note that "conda" can cooperate with "pip" and "pypi" to avoid conflicts. I think it would be useful for "conda" to be aware of any conflicting packages managed by "apt" in a similar way. The same problem also occurs when managing packages directly using R, which conflict with packages managed by "apt", but this can be mitigated to some extent by managing R in isolated "conda" environments instead of "apt" packages.



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