Commit d0391ce9 authored by Paul McCarthy's avatar Paul McCarthy 🚵
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DOC: Note about base_environment

parent 4149af80
......@@ -7,7 +7,10 @@ An official FSL installation is a self-contained directory installed on an end u
> <sup>*</sup> The [conda documentation](https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html#managing-envs) recommends against installing packages into a base conda environment, therefore `$FSLDIR` is created as a child environment.
By default, the base miniconda environment is installed into `$FSLDIR/../.fslconda/` (i.e. `/usr/local/.fslconda/`, if the default setting of `FSLDIR=/usr/local/fsl/` is used)<sup>*</sup>.
An official (`fslinstaller`-installed) FSL installation can be distinguished from a manually installed/managed FSL installation by the presence of a file called `$FSLDIR/share/fsl/base_environment`. This file is created by the `fslinstaller` script, and is a plain-text file which contains the location of the base miniconda environment.
By default, the base miniconda environment is installed into `$FSLDIR/../.fslconda/` (i.e. `/usr/local/.fslconda/`, if the default setting of `FSLDIR=/usr/local/fsl/` is used), but this can be overridden by the user<sup>*</sup>.
> <sup>*</sup> The only possible options for the base/child environment locations are either to have them in separate directories, or to have the child environment directory located within the base environment directory. The former option was chosen, as the latter option would require a system of links to be created from `$FSLDIR/*` into `$FSLDIR/<child-environment>/*`.
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