diff --git a/container-files/Dockerfile-fre-cli b/container-files/Dockerfile-fre-cli
index 4557e761d..8df8e7c86 100644
--- a/container-files/Dockerfile-fre-cli
+++ b/container-files/Dockerfile-fre-cli
@@ -18,13 +18,17 @@ RUN apt update \
 RUN conda update -n base -c conda-forge conda
 
 # Copy runscript in container and make it executable
-COPY container-files/runscript.sh /app/exec/runscript.sh
+COPY runscript.sh /app/exec/runscript.sh
 RUN chmod +x /app/exec/runscript.sh
 
 # Set up conda environment directory for cylc workflow
-COPY container-files/cylc-flow-tools.yaml ${conda_location}/cylc-flow-tools.yaml
+COPY cylc-flow-tools.yaml ${conda_location}/cylc-flow-tools.yaml
 RUN mamba env create --file ${conda_location}/cylc-flow-tools.yaml -p ${conda_location}
 
+## NOT IDEAL but these changes are needed for the hsm conda package (specifically hsmput.mk) to work 
+RUN sed -i '28p' /app/cylc-flow-tools/mk/hsmput.mk
+RUN sed -i 's/>& \/dev\/null/> \/dev\/null 2>\&1/g' /app/cylc-flow-tools/mk/hsmput.mk
+
 # Maybe perhaps tag an external mounted volume /mnt2 as being safe...
 # RUN git config --global --add safe.directory /mnt2
 
diff --git a/container-files/cylc-flow-tools.yaml b/container-files/cylc-flow-tools.yaml
index a394c4e83..a1a2a7141 100644
--- a/container-files/cylc-flow-tools.yaml
+++ b/container-files/cylc-flow-tools.yaml
@@ -4,7 +4,7 @@ channels:
   - NOAA-GFDL
 dependencies:
   - noaa-gfdl::hsm
-  - noaa-gfdl::fre-cli==2025.04
+  - noaa-gfdl::fre-cli==2026.01.alpha2
   - conda-forge::nco
   - conda-forge::rsync
   - conda-forge::make