Commit aaf078bb authored by Michiel Cottaar's avatar Michiel Cottaar
Browse files

Updated instructions to reflect jupyter notebook is already installed

parent c4dd82c1
...@@ -24,36 +24,13 @@ installed. ...@@ -24,36 +24,13 @@ installed.
## For attendees ## For attendees
To run these notebooks in the `fslpython` environment, you must first install These notebooks can be run in the `fslpython` environment using:
jupyter:
```
# If your FSL installation requires administrative privileges to modify, then
# you MUST run these commands as root - don't just prefix each individual
# command with sudo, or you will probably install jupyter into the wrong
# location!
#
# One further complication - once you have become root, $FSLDIR may not be set,
# so either set it as we have done below, or make sure that it is set, before
# proceeding.
sudo su
export FSLDIR=/usr/local/fsl
source $FSLDIR/fslpython/bin/activate fslpython
conda install jupyter
source deactivate
ln -s $FSLDIR/fslpython/envs/fslpython/bin/jupyter $FSLDIR/bin/fsljupyter
```
Then, clone this repository on your local machine, and run
`fsljupyter notebook`:
``` ```
git clone git@git.fmrib.ox.ac.uk:fsl/pytreat-2018-practicals.git git clone git@git.fmrib.ox.ac.uk:fsl/pytreat-2018-practicals.git
cd pytreat-2018-practicals cd pytreat-2018-practicals
fsljupyter notebook fslpython -m notebook
``` ```
...@@ -110,17 +87,14 @@ To contribute to the practicals: ...@@ -110,17 +87,14 @@ To contribute to the practicals:
repository. repository.
When you install `jupyter` above, you may also wish to install You may also wish to install
[`notedown`](https://github.com/aaren/notedown): [`notedown`](https://github.com/aaren/notedown):
``` ```
# . source $FSLDIR/fslpython/bin/activate fslpython
# see instructions above
# .
conda install jupyter
pip install notedown pip install notedown
source deactivate source deactivate
ln -s $FSLDIR/fslpython/envs/fslpython/bin/jupyter $FSLDIR/bin/fsljupyter fslpython -m notedown
ln -s $FSLDIR/fslpython/envs/fslpython/bin/notedown $FSLDIR/bin/fslnotedown ln -s $FSLDIR/fslpython/envs/fslpython/bin/notedown $FSLDIR/bin/fslnotedown
``` ```
......
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