From 608fa419068d867b75e08d8339762843f3530e3a Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 25 Nov 2025 10:00:38 +0100 Subject: [PATCH 1/3] admin training: use miniforge even if correctly configured the base environment will be constructed using the defaults channel ... which is problematic with the TOS https://codebase.helmholtz.cloud/m.bernt/conda-recommendations --- topics/admin/tutorials/ansible-galaxy/tutorial.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/topics/admin/tutorials/ansible-galaxy/tutorial.md b/topics/admin/tutorials/ansible-galaxy/tutorial.md index edcad9bb2e129b..0a4d5aed23736e 100644 --- a/topics/admin/tutorials/ansible-galaxy/tutorial.md +++ b/topics/admin/tutorials/ansible-galaxy/tutorial.md @@ -936,7 +936,7 @@ The configuration is quite simple thanks to the many sensible defaults that are > `galaxy_client_use_prebuilt` | `true` | We are going to use a prebuilt client to save some time during this tutorial, if you want you can set it to false later and see how galaxy starts building the client itself. > `miniconda_prefix` | {% raw %}`"{{ galaxy_tool_dependency_dir }}/_conda"`{% endraw %} | We will manually install conda as well. Normally Galaxy will attempt to auto-install this, but since we will set up a production-ready instance with multiple handlers, there is the chance that they can become deadlocked. > `miniconda_version` | `25.3` | Install a specific miniconda version, the latest one at the time of writing that was tested and working. -> `miniconda_distribution` | `miniconda` | Install a specific distribution of miniconda, such as `miniforge` (default), `micromamba`, `miniconda` or `anaconda`. This determines the default value for the `miniconda_executable` (`mamba` for `miniforge`) +> `miniconda_distribution` | `miniforge` | Install a specific distribution of miniconda, such as `miniforge` (default), `micromamba`, `miniconda` or `anaconda`. This determines the default value for the `miniconda_executable` (`mamba` for `miniforge`) > `miniconda_channels` ` | `['conda-forge']` | Use the free and community-maintained `conda-forge` channel. > > > Different Galaxy Releases! @@ -965,11 +965,11 @@ The configuration is quite simple thanks to the many sensible defaults that are > +galaxy_force_checkout: true > +miniconda_prefix: "{{ galaxy_tool_dependency_dir }}/_conda" > +miniconda_version: 25.3 -> +miniconda_distribution: miniconda +> +miniconda_distribution: miniforge > +miniconda_channels: ['conda-forge'] > {% endraw %} > ``` -> {: data-commit="Configure miniconda and galaxy"} +> {: data-commit="Configure miniforge and galaxy"} > > > Following this training outside of a GAT course? > > Consider updating the Galaxy Commit ID to the latest version of Galaxy available, this will probably give better results (given that dependencies are always updating) than using a potentially outdated version. From 5a16d0212159618436327db4e420a1cccdfc89fb Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 25 Nov 2025 10:56:23 +0100 Subject: [PATCH 2/3] update docs around conda Since the alternatives are not real alternatives anymore, the link to the docs should be sufficient. - Micromamba uses just the conda-forge binaries - Mambaforge is miniforge - miniconda and anaconda should not be used (TOS) --- topics/admin/tutorials/ansible-galaxy/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/admin/tutorials/ansible-galaxy/tutorial.md b/topics/admin/tutorials/ansible-galaxy/tutorial.md index 0a4d5aed23736e..6625f4a14d3dc1 100644 --- a/topics/admin/tutorials/ansible-galaxy/tutorial.md +++ b/topics/admin/tutorials/ansible-galaxy/tutorial.md @@ -936,7 +936,7 @@ The configuration is quite simple thanks to the many sensible defaults that are > `galaxy_client_use_prebuilt` | `true` | We are going to use a prebuilt client to save some time during this tutorial, if you want you can set it to false later and see how galaxy starts building the client itself. > `miniconda_prefix` | {% raw %}`"{{ galaxy_tool_dependency_dir }}/_conda"`{% endraw %} | We will manually install conda as well. Normally Galaxy will attempt to auto-install this, but since we will set up a production-ready instance with multiple handlers, there is the chance that they can become deadlocked. > `miniconda_version` | `25.3` | Install a specific miniconda version, the latest one at the time of writing that was tested and working. -> `miniconda_distribution` | `miniforge` | Install a specific distribution of miniconda, such as `miniforge` (default), `micromamba`, `miniconda` or `anaconda`. This determines the default value for the `miniconda_executable` (`mamba` for `miniforge`) +> `miniconda_distribution` | `miniforge` | Install a specific distribution of conda, see https://github.com/galaxyproject/ansible-miniconda for alternatives. This determines the default value for the `miniconda_executable` (`conda` for `miniforge`) > `miniconda_channels` ` | `['conda-forge']` | Use the free and community-maintained `conda-forge` channel. > > > Different Galaxy Releases! From cc1af28ffa70dff1b33dddb52f8893b41861329f Mon Sep 17 00:00:00 2001 From: Mira Kuntz Date: Thu, 27 Nov 2025 12:02:59 +0100 Subject: [PATCH 3/3] git-gat knitting --- topics/admin/tutorials/ansible-galaxy/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/admin/tutorials/ansible-galaxy/tutorial.md b/topics/admin/tutorials/ansible-galaxy/tutorial.md index 6625f4a14d3dc1..6bfc3830c888a5 100644 --- a/topics/admin/tutorials/ansible-galaxy/tutorial.md +++ b/topics/admin/tutorials/ansible-galaxy/tutorial.md @@ -998,7 +998,7 @@ The configuration is quite simple thanks to the many sensible defaults that are > +++ b/group_vars/galaxyservers.yml > @@ -13,3 +13,17 @@ miniconda_prefix: "{{ galaxy_tool_dependency_dir }}/_conda" > miniconda_version: 25.3 -> miniconda_distribution: miniconda +> miniconda_distribution: miniforge > miniconda_channels: ['conda-forge'] > + > +galaxy_config: @@ -2282,7 +2282,7 @@ Finally, we have explicitly mapped the `local` class of tools to run in the `loc > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml > @@ -14,6 +14,24 @@ miniconda_version: 25.3 -> miniconda_distribution: miniconda +> miniconda_distribution: miniforge > miniconda_channels: ['conda-forge'] > > +# Galaxy Job Configuration