modified instructions on conda environment

brainglobe · Jun 21, 2024 · 871d194 · 871d194
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Showing 5 changed files with 10 additions and 11 deletions.
diff --git a/README.md b/README.md
@@ -45,7 +45,7 @@ Build unbiased anatomical templates from individual images
   ```sh
   git clone --recursive https://github.com/CoBrALab/  optimized_antsMultivariateTemplateConstruction.git
   cd optimized_antsMultivariateTemplateConstruction
-  echo "export PATH=$(pwd):$PATH" >> $HOME/.bashrc
+  echo "export PATH=$(pwd):\$PATH" >> $HOME/.bashrc
   source $HOME/.bashrc  # or restart your terminal
   ```
 
@@ -58,15 +58,18 @@ We recommend installing `brainglobe-template-builder` within a [conda](https://d
 
 
 ```sh
-conda create -n template-builder -c conda-forge python=3.11 pip parallel qbatch simpleitk vtk
+conda env create -n template-builder -f environment.yaml
 conda activate template-builder
 ```
 
 We have called the environment "template-builder", but you can choose any name you like.
 
+This environment contains all dependencies for running the optimised ANTs template construction pipeline, but if you want to use the pre- and
+post-processing funcitonalities of `brainglobe-template-builder`, you will need to also pip install the package in editable mode (see below).
+
 ### Install `brainglobe-template-builder` with `pip`
 
-```sh
+
 To install the latest development version of `brainglobe-template-builder`, first clone the repository:
 
 ```sh

diff --git a/examples/cobralab_environment.yaml → environment.yaml b/examples/cobralab_environment.yaml → environment.yaml
@@ -1,12 +1,10 @@
-name: cobralab
 channels:
   - conda-forge
 dependencies:
   - python=3.11
   - pip
   - parallel
   - qbatch
+  - scipy
   - simpleitk
   - vtk
-  - vtk-base
-  - vtk-io-ffmpeg
diff --git a/examples/slurm_batch_across_average_types.sh b/examples/slurm_batch_across_average_types.sh
@@ -16,8 +16,8 @@
 module load miniconda
 module load ants
 
-# Activate the conda environmen
-conda activate cobralab
+# Activate the conda environment
+conda activate template-builder
 
 # Define the atlas-forge directory and species name
 ATLAS_DIR="/ceph/neuroinformatics/neuroinformatics/atlas-forge"

diff --git a/examples/slurm_batch_across_templates.sh b/examples/slurm_batch_across_templates.sh
@@ -15,7 +15,7 @@
 # Load the required modules
 module load miniconda
 module load ants
-# Activate the conda environment (becaue we need parallel and qbatch)
+# Activate the conda environment
 conda activate template-builder
 
 # Define the atlas-forge directory and species name

diff --git a/pyproject.toml b/pyproject.toml
@@ -24,8 +24,6 @@ dependencies = [
     "brainglobe-utils>=0.5",
     "brainglobe-atlasapi>=2.0.7",
     "loguru",
-    "simpleitk",
-    "vtk",
     "antspyx",
 ]