local_development.md

# Setting up a local FSL development environment


*This document is written under the assumption that you have FSL 6.0.6 or
newer, installed via the fslinstaller script. These instructions will not work
for older versions of FSL, nor for manually managed FSL installations.*


This document describes how to set up a local development environment for
compiling FSL C/C++ projects. It does **not** describe how to build conda
packages for FSL projects - this is described in
[`building_fsl_conda_packages.md`](building_fsl_conda_packages.md).


A standard FSL installation comes with the `Makefile` machinery required to
compile FSL C/C++ projects. All that you need to add is a C/C++ compiler. You
can use your operating system compiler if you wish, but be warned that doing
so will potentially compile your code in a different way to how the official
FSL conda packages have been compiled.


A better option is to use the [conda-forge](https://conda-forge.org/) compiler
toolchain. You can install the conda-forge compilers directly into `$FSLDIR`
like so:


```bash
# Set up your environment for FSL development.
export PATH=$FSLDIR/bin:$PATH
source $FSLDIR/etc/fslconf/fsl-devel.sh

# Install the conda-forge C/C++ compiler toolchain and GNU Make
conda install -c conda-forge c-compiler cxx-compiler make
```

Now, when you want to work on a FSL project, you can follow these steps:


```bash
# Configure your environment for FSL development
source $FSLDIR/etc/fslconf/fsl-devel.sh

# Get a copy of the source
git clone https://git.fmrib.ox.ac.uk/fsl/randomise.git
cd randomise

# Or work with the version you have installed
cd $FSLDIR/src/fsl-randomise/

# compile
make

# Re-install into your existing $FSLDIR
make install

# Or install into a different prefix
export FSLDEVDIR=/my/local/dev/prefix
make install
```