Commit 5f51d701 authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

DOC: Small fixes

parent 1fcf3765
......@@ -14,7 +14,7 @@ By default, the base miniconda environment is installed into `$FSLDIR/../.fslcon
Because `$FSLDIR` is a conda environment into which all FSL projects and their dependencies are installed, `$FSLDIR/bin/` will contain executable files provided by both FSL, and by its dependencies. This can give rise to a problem whereby executables in `$FSLDIR/bin/` can mask other executables of the same name which are also installed in the user's environment, but come after `$FSLDIR/bin/` on the user's `$PATH` (e.g. `python`, `conda`, etc).
To work around this problem, and to isolate all of the FSL executables from the other executables installed into the same environment, the conda packages for all FSL projects use [`post-link.sh` and `pre-unlink.sh`](https://docs.conda.io/projects/conda-build/en/latest/resources/link-scripts.html) scripts to create "wrapper scripts" within `$FSLDIR/share/fsl/bin/`<sup>*</sup>. These wrapper scripts are created by the [`$FSLDIR/share/fsl/sbin/createFSLWrapper`](https://git.fmrib.ox.ac.uk/fsl/base/-/blob/master/share/fsl/sbin/createFSLWrapper) script, which is installed as part of the [`fsl-base`]((https://git.fmrib.ox.ac.uk/fsl/base/) package.
To work around this problem, and to isolate all of the FSL executables from the other executables installed into the same environment, the conda packages for all FSL projects use [`post-link.sh` and `pre-unlink.sh`](https://docs.conda.io/projects/conda-build/en/latest/resources/link-scripts.html) scripts to create _wrapper scripts_ within `$FSLDIR/share/fsl/bin/`<sup>*</sup>. These wrapper scripts are created by the [`$FSLDIR/share/fsl/sbin/createFSLWrapper`](https://git.fmrib.ox.ac.uk/fsl/base/-/blob/master/share/fsl/sbin/createFSLWrapper) script, which is installed as part of the [`fsl-base`](https://git.fmrib.ox.ac.uk/fsl/base/) package.
> <sup>*</sup> More details on FSL project conda recipes are outlined in [`fsl_conda_recipes.md`](fsl_conda_recipes.md).
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment