From 09d6a0a133cbcd3468a7ad26014612beef137399 Mon Sep 17 00:00:00 2001
From: Neurodesk Github Action Runner <mail.neurodesk@gmail.com>
Date: Mon, 4 Nov 2024 06:58:29 +0000
Subject: [PATCH] skipci

---
 recipes/freesurfer/build.sh  | 16 +++++++++++-----
 recipes/freesurfer/test.sh   |  1 +
 recipes/quickshear/README.md |  4 ++--
 3 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/recipes/freesurfer/build.sh b/recipes/freesurfer/build.sh
index 5a954cfc..d042e78e 100644
--- a/recipes/freesurfer/build.sh
+++ b/recipes/freesurfer/build.sh
@@ -8,9 +8,9 @@ if [ "$1" != "" ]; then
 fi
 
 export toolName='freesurfer'
-export toolVersion=7.3.2
+export toolVersion=7.4.1
 
-source ../main_setup.sh
+source ../main_setup.sh --reinstall_neurodocker=false
 
 neurodocker generate ${neurodocker_buildMode} \
    --base-image centos:8 \
@@ -18,9 +18,6 @@ neurodocker generate ${neurodocker_buildMode} \
    --run="printf '#!/bin/bash\nls -la' > /usr/bin/ll" \
    --run="chmod +x /usr/bin/ll" \
    --run="mkdir -p ${mountPointList}" \
-   --run="cd /etc/yum.repos.d/" \
-   --run="sed -i 's/mirrorlist/#mirrorlist/g' /etc/yum.repos.d/CentOS-*" \
-   --run="sed -i 's|#baseurl=http://mirror.centos.org|baseurl=http://vault.centos.org|g' /etc/yum.repos.d/CentOS-*" \
    --run="yum upgrade -y dnf" \
    --run="yum upgrade -y rpm" \
    --install wget \
@@ -64,10 +61,19 @@ neurodocker generate ${neurodocker_buildMode} \
    --copy license.txt /opt/${toolName}-${toolVersion}/license.txt \
   > ${imageName}.${neurodocker_buildExt}
 
+# Hack to make CENTOS8 work with neurodocker
+sed -i '4i RUN sed -i '\''s/mirrorlist/#mirrorlist/g'\'' /etc/yum.repos.d/CentOS-*' ${imageName}.${neurodocker_buildExt}
+sed -i '5i RUN sed -i '\''s|#baseurl=http://mirror.centos.org|baseurl=http://vault.centos.org|g'\'' /etc/yum.repos.d/CentOS-*' ${imageName}.${neurodocker_buildExt}
+
+sed -i '/ENV LANG="en_US.UTF-8" \\/,+2d' ${imageName}.${neurodocker_buildExt}
+sed -i '/localedef \\/d' ${imageName}.${neurodocker_buildExt}
+sed -i '/&& localedef -i en_US -f UTF-8 en_US.UTF-8 \\/d' ${imageName}.${neurodocker_buildExt}
+
 if [ "$1" != "" ]; then
    ./../main_build.sh
 fi
 
+
 # debug segmentSubjectT1_autoEstimateAlveusML:
 # dnf install strace -y
 # strace segmentSubjectT1_autoEstimateAlveusML
diff --git a/recipes/freesurfer/test.sh b/recipes/freesurfer/test.sh
index a24ac65a..53611916 100644
--- a/recipes/freesurfer/test.sh
+++ b/recipes/freesurfer/test.sh
@@ -1,6 +1,7 @@
 segmentSubjectT1_autoEstimateAlveusML #should not complain about libraries missing
 checkMCR.sh #should not complain
 segmentThalamicNuclei.sh --help #should not compalin about matlab libraries missing
+mris_left_right_register # should not through permission denied error
 
 # interactive test:
 if [[ -v DISPLAY ]]; then
diff --git a/recipes/quickshear/README.md b/recipes/quickshear/README.md
index 1095f4b4..8bb975d0 100644
--- a/recipes/quickshear/README.md
+++ b/recipes/quickshear/README.md
@@ -1,6 +1,6 @@
 
 ----------------------------------
-## quickshear/1.1.0 ##
+## quickshear/toolVersion ##
 Quickshear uses a skull stripped version of an anatomical image as a reference to deface the unaltered anatomical image.
 
 Example:
@@ -12,7 +12,7 @@ quickshear input.nii.gz mask.nii.gz defaced.nii.gz
 
 More documentation can be found here: [link_to_documentation](https://github.com/nipy/quickshear)
 
-To make the executables and scripts inside this container transparently available in the command line of environments where Neurocommand is installed: ml quickshear/1.1.0
+To make the executables and scripts inside this container transparently available in the command line of environments where Neurocommand is installed: ml quickshear/toolVersion
 
 Citation:
 ```