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:
#!/bin/bash
#@(#)bioconda3.sh 2019-02-23 A.J.Travis
#
# Wrapper for Bioconda Python environment
#
exec /bin/bash --rcfile /usr/local/bin/bioconda3.rc
#!/bin/bash
#@(#)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.
HTH,
Tony.
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