From 9d4ecea76d0ca4f56e5746098c7203f59a665986 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 19 Jul 2023 17:09:54 -0400
Subject: [PATCH] MNT: Install ANTs from conda-forge

---
 Dockerfile | 13 -------------
 env.yml    |  2 ++
 2 files changed, 2 insertions(+), 13 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 38f549eb9..a3ec960ee 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -77,13 +77,6 @@ RUN mkdir -p /opt/afni-latest \
         -name "3dAutomask" -or \
         -name "3dvolreg" \) -delete
 
-# ANTs 2.4.4
-FROM downloader as ants
-RUN mkdir -p /opt && \
-    curl -sSLO "https://github.com/ANTsX/ANTs/releases/download/v2.4.4/ants-2.4.4-ubuntu-22.04-X64-gcc.zip" && \
-    unzip ants-2.4.4-ubuntu-22.04-X64-gcc.zip -d /opt && \
-    rm ants-2.4.4-ubuntu-22.04-X64-gcc.zip
-
 # Connectome Workbench 1.5.0
 FROM downloader as workbench
 RUN mkdir /opt/workbench && \
@@ -172,7 +165,6 @@ RUN apt-get update -qq \
 # Install files from stages
 COPY --from=freesurfer /opt/freesurfer /opt/freesurfer
 COPY --from=afni /opt/afni-latest /opt/afni-latest
-COPY --from=ants /opt/ants-2.4.4 /opt/ants
 COPY --from=workbench /opt/workbench /opt/workbench
 
 # Simulate SetUpFreeSurfer.sh
@@ -197,11 +189,6 @@ ENV PATH="/opt/afni-latest:$PATH" \
     AFNI_IMSAVE_WARNINGS="NO" \
     AFNI_PLUGINPATH="/opt/afni-latest"
 
-# ANTs config
-ENV ANTSPATH="/opt/ants" \
-    PATH="/opt/ants/bin:$PATH" \
-    LD_LIBRARY_PATH="/opt/ants/lib:$LD_LIBRARY_PATH"
-
 # Workbench config
 ENV PATH="/opt/workbench/bin_linux64:$PATH" \
     LD_LIBRARY_PATH="/opt/workbench/lib_linux64:$LD_LIBRARY_PATH"
diff --git a/env.yml b/env.yml
index 6eacbfd16..8c5229d70 100644
--- a/env.yml
+++ b/env.yml
@@ -26,6 +26,8 @@ dependencies:
   # Workflow dependencies: Convert3D
   - convert3d=1.3.0
   - libitk=5.2  # 5.3 fails with c3d
+  # Workflow dependencies: ANTs
+  - ants=2.4.4
   # Workflow dependencies: FSL (versions pinned in 6.0.6.2)
   - fsl-bet2=2111.0
   - fsl-flirt=2111.0